Variant Detail

Variant Information
ID
DPV: 2143
Chromosome
1
Gene
HGVS (GRCh37/hg19)
NC_000001.10:g.115256530G>T
HGVS (GRCh38/hg38)
NC_000001.11:g.114713909G>T
HGVS (RNA)
NM_002524.3:c.181C>A
HGVS (Protein)
NP_002515.1:p.Q61K
dbSNP
-
ClinGen Allele Registry
CA151263
Allele Frequency
Individual Information

ID
DPVS:2002.3
Clinical Significance
Pathogenic
Date Last Evaluated
2018-05-30
Clinical Significance Citation
-
Transcript
-
Disease

Phenotype
-
Zygosity
single heterozygote
Allele Origin
somatic
Affected Status
yes
Sample Type
  • DNA
Analysis Type
  • SEQuencing
Collection Method
clinical testing
Compound heterozygous variant(s)
Data Submitter
Comment
This variant was detected in  IRUD (Initiative on Rare and Undiagnosed Diseases) project.

ClinVar
Model Animals
VCF
VCF (GRCh37/hg19) 
											##fileformat=VCFv4.0
##reference=GRCh37
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##INFO=<ID=CLNDISDB,Number=.,Type=String,Description="Tag-value pairs of disease database name and identifier, e.g. OMIM:NNNNNN (from ClinVar)">
##INFO=<ID=CLNDN,Number=.,Type=String,Description="ClinVar's preferred disease name for the concept specified by disease identifiers in CLNDISDB (from ClinVar)">
##INFO=<ID=CLNHGVS,Number=.,Type=String,Description="Top-level (primary assembly, alt, or patch) HGVS expression.(from ClinVar)">
##INFO=<ID=CLNSIG,Number=.,Type=String,Description="Clinical significance for this single variant (from ClinVar)">
##INFO=<ID=EXAC_AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed (from ExAC r1)">
##INFO=<ID=EXAC_AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed (from ExAC r1)">
##INFO=<ID=EXAC_AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes (from ExAC r1)">
##INFO=<ID=EXAC_FILTER,Number=1,Type=String,Description="calculated by self of overlapping values in field FILTER (from ExAC r1)">
##INFO=<ID=GNOMAD_AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed (from gnomAD v2.1.1 )">
##INFO=<ID=GNOMAD_AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed (from gnomAD v2.1.1 )">
##INFO=<ID=GNOMAD_AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes (from gnomAD v2.1.1 )">
##INFO=<ID=HGVD_AAF,Number=A,Type=Float,Description="Alternative Allele Frequency(s) NA/(NR+NAtotal) (from HGVD/DBexome20170802)">
##INFO=<ID=HGVD_AC,Number=A,Type=Integer,Description="number(s) of alternative allele(s) (from HGVD/DBexome20170802)">
##INFO=<ID=HGVD_NR,Number=1,Type=Integer,Description="number of reference allele (from HGVD/DBexome20170802)">
##INFO=<ID=TOMMO_4_7K_AC,Number=A,Type=Integer,Description="Allele count in genotypes (from ToMMo 4.7KJPN (20190826))">
##INFO=<ID=TOMMO_4_7K_AF,Number=A,Type=Float,Description="Allele frequency, for each ALT allele, in the same order as listed  (from ToMMo 4.7KJPN (20190826))">
##INFO=<ID=TOMMO_4_7K_AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes (from ToMMo 4.7KJPN (20190826))">
##INFO=<ID=dbSNP_RSID,Number=1,Type=String,Description="dbSNP ID (from dbSNP b151 )">
##INFO=<ID=GENEINFO,Number=1,Type=String,Description="Pairs each of gene symbol:gene id. The gene symbol and id are delimited by a colon (:)">
##INFO=<ID=DPVID,Number=.,Type=String,Description="DPV Variant ID">
##INFO=<ID=DPVSIG,Number=.,Type=String,Description="Variant Clinical Significance">
##INFO=<ID=DPVDSDBID,Number=.,Type=String,Description="Variant disease database ID">
##INFO=<ID=DPVDBN,Number=.,Type=String,Description="Variant disease name">
##INFO=<ID=DPVHGVS,Number=.,Type=String,Description="Variant in HGVS.">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
1	115256530	NC_000001.10:g.115256530G>T	G	T	.	.	GNOMAD_AF=0;GNOMAD_AC=0;GNOMAD_AN=251378;CLNALLELEID=83949;CLNDN=RAS_Inhibitor_response|Vascular_Tumors_Including_Pyogenic_Granuloma|Hepatocellular_carcinoma|Acute_myeloid_leukemia|Melanoma|Adrenocortical_carcinoma|Neuroblastoma|Chronic_lymphocytic_leukemia|Large_congenital_melanocytic_nevus|Transitional_cell_carcinoma_of_the_bladder|Multiple_myeloma|Renal_cell_carcinoma,_papillary,_1|Malignant_melanoma_of_skin|Lung_adenocarcinoma|Non-small_cell_lung_cancer|Neoplasm_of_brain|Nasopharyngeal_Neoplasms|Neoplasm_of_the_large_intestine|Adenocarcinoma_of_stomach|Ovarian_Serous_Cystadenocarcinoma|Neurocutaneous_melanocytosis|Glioblastoma|Rasopathy|Malignant_neoplasm_of_body_of_uterus|not_provided;CLNDISDB=.|.|Human_Phenotype_Ontology:HP:0001402,Human_Phenotype_Ontology:HP:0002899,Human_Phenotype_Ontology:HP:0003007,Human_Phenotype_Ontology:HP:0006750,MedGen:C2239176,OMIM:114550,Orphanet:ORPHA88673,SNOMED_CT:187769009,SNOMED_CT:25370001|Human_Phenotype_Ontology:HP:0001914,Human_Phenotype_Ontology:HP:0004808,Human_Phenotype_Ontology:HP:0004843,Human_Phenotype_Ontology:HP:0005516,Human_Phenotype_Ontology:HP:0006724,Human_Phenotype_Ontology:HP:0006728,MONDO:MONDO:0018874,MeSH:D015470,MedGen:C0023467,OMIM:601626,Orphanet:ORPHA519,SNOMED_CT:17788007|Human_Phenotype_Ontology:HP:0002861,Human_Phenotype_Ontology:HP:0002887,Human_Phenotype_Ontology:HP:0006777,Human_Phenotype_Ontology:HP:0007474,MONDO:MONDO:0005105,MeSH:D008545,MedGen:C0025202,SNOMED_CT:2092003,SNOMED_CT:372244006|Human_Phenotype_Ontology:HP:0002889,Human_Phenotype_Ontology:HP:0006744,Human_Phenotype_Ontology:HP:0006759,MONDO:MONDO:0006639,MeSH:D018268,MedGen:C0206686|Human_Phenotype_Ontology:HP:0003006,Human_Phenotype_Ontology:HP:0006738,MONDO:MONDO:0005072,MeSH:D009447,MedGen:C0027819,Orphanet:ORPHA635,SNOMED_CT:87364003|Human_Phenotype_Ontology:HP:0005550,Human_Phenotype_Ontology:HP:0006734,Human_Phenotype_Ontology:HP:0006760,MONDO:MONDO:0004948,MeSH:D015451,MedGen:C0023434,OMIM:151400,Orphanet:ORPHA67038,SNOMED_CT:277473004,SNOMED_CT:51092000|Human_Phenotype_Ontology:HP:0005600,Human_Phenotype_Ontology:HP:0005604,MONDO:MONDO:0044792,MedGen:C1842036,OMIM:137550,Orphanet:ORPHA626|Human_Phenotype_Ontology:HP:0006740,MONDO:MONDO:0005611,MedGen:C0279680|Human_Phenotype_Ontology:HP:0006775,MONDO:MONDO:0009693,MeSH:D009101,MedGen:C0026764,OMIM:254500,Orphanet:ORPHA29073,SNOMED_CT:109989006,SNOMED_CT:55921005|Human_Phenotype_Ontology:HP:0011797,MedGen:C1336839,OMIM:605074|Human_Phenotype_Ontology:HP:0012056,MONDO:MONDO:0005012,MeSH:C562393,MedGen:C0151779,SNOMED_CT:93655004|Human_Phenotype_Ontology:HP:0030078,MONDO:MONDO:0005061,MeSH:D000077192,MedGen:C0152013|Human_Phenotype_Ontology:HP:0030358,MONDO:MONDO:0005233,MeSH:D002289,MedGen:C0007131,SNOMED_CT:254637007|Human_Phenotype_Ontology:HP:0030692,MONDO:MONDO:0021211,MeSH:D001932,MedGen:C0006118,SNOMED_CT:126952004|Human_Phenotype_Ontology:HP:0100630,MONDO:MONDO:0005375,MeSH:D009303,MedGen:C0027439|Human_Phenotype_Ontology:HP:0100834,MeSH:D015179,MedGen:C0009404,SNOMED_CT:126837005|MONDO:MONDO:0005036,MedGen:C0278701|MONDO:MONDO:0006046,MedGen:C0279663|MONDO:MONDO:0009578,MedGen:C0544862,OMIM:249400,Orphanet:ORPHA2481|MONDO:MONDO:0018177,MeSH:D005909,MedGen:C0017636,Orphanet:ORPHA360,SNOMED_CT:63634009|MONDO:MONDO:0021060,MedGen:CN166718,Orphanet:ORPHA536391|MedGen:C0153574|MedGen:CN517202;CLNSIG=Conflicting_interpretations_of_pathogenicity;CLNHGVS=NC_000001.10:g.115256530G>T;GENEINFO=7989:4893;DPVID=2143;DPVSIG=Pathogenic;DPVDSDBID=OMIM:137550;DPVDBN=Spitz_nevus;DPVHGVS=NC_000001.10:g.115256530G>T	.
VCF (GRCh38/hg38) 
											##fileformat=VCFv4.0
##reference=GRCh38
##INFO=<ID=CLNALLELEID,Number=1,Type=Integer,Description="the ClinVar Allele ID">
##INFO=<ID=CLNDISDB,Number=.,Type=String,Description="Tag-value pairs of disease database name and identifier, e.g. OMIM:NNNNNN (from ClinVar)">
##INFO=<ID=CLNDN,Number=.,Type=String,Description="ClinVar's preferred disease name for the concept specified by disease identifiers in CLNDISDB (from ClinVar)">
##INFO=<ID=CLNHGVS,Number=.,Type=String,Description="Top-level (primary assembly, alt, or patch) HGVS expression.(from ClinVar)">
##INFO=<ID=CLNSIG,Number=.,Type=String,Description="Clinical significance for this single variant (from ClinVar)">
##INFO=<ID=GNOMAD_AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed (from gnomAD v2.1.1 )">
##INFO=<ID=GNOMAD_AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed (from gnomAD v2.1.1 )">
##INFO=<ID=GNOMAD_AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes (from gnomAD v2.1.1 )">
##INFO=<ID=dbSNP_RSID,Number=1,Type=String,Description="dbSNP ID (from dbSNP b151 )">
##originalFile=</tmp/crossmap-input-6vhezq5d>
##targetRefGenome=</usr/lib64/python2.7/site-packages/transvar/transvar.download/hg38.fa>
##INFO=<ID=GENEINFO,Number=1,Type=String,Description="Pairs each of gene symbol:gene id. The gene symbol and id are delimited by a colon (:)">
##INFO=<ID=DPVID,Number=.,Type=String,Description="DPV Variant ID">
##INFO=<ID=DPVSIG,Number=.,Type=String,Description="Variant Clinical Significance">
##INFO=<ID=DPVDSDBID,Number=.,Type=String,Description="Variant disease database ID">
##INFO=<ID=DPVDBN,Number=.,Type=String,Description="Variant disease name">
##INFO=<ID=DPVHGVS,Number=.,Type=String,Description="Variant in HGVS.">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
1	114713909	NC_000001.10:g.115256530G>T	G	T	.	.	dbSNP_RSID=rs121913254;GNOMAD_AF=0;GNOMAD_AC=0;GNOMAD_AN=251378;CLNALLELEID=83949;CLNDN=RAS_Inhibitor_response|Vascular_Tumors_Including_Pyogenic_Granuloma|Hepatocellular_carcinoma|Acute_myeloid_leukemia|Melanoma|Adrenocortical_carcinoma|Neuroblastoma|Chronic_lymphocytic_leukemia|Large_congenital_melanocytic_nevus|Transitional_cell_carcinoma_of_the_bladder|Multiple_myeloma|Renal_cell_carcinoma,_papillary,_1|Malignant_melanoma_of_skin|Lung_adenocarcinoma|Non-small_cell_lung_cancer|Neoplasm_of_brain|Nasopharyngeal_Neoplasms|Neoplasm_of_the_large_intestine|Adenocarcinoma_of_stomach|Ovarian_Serous_Cystadenocarcinoma|Neurocutaneous_melanocytosis|Glioblastoma|Rasopathy|Malignant_neoplasm_of_body_of_uterus|not_provided;CLNDISDB=.|.|Human_Phenotype_Ontology:HP:0001402,Human_Phenotype_Ontology:HP:0002899,Human_Phenotype_Ontology:HP:0003007,Human_Phenotype_Ontology:HP:0006750,MedGen:C2239176,OMIM:114550,Orphanet:ORPHA88673,SNOMED_CT:187769009,SNOMED_CT:25370001|Human_Phenotype_Ontology:HP:0001914,Human_Phenotype_Ontology:HP:0004808,Human_Phenotype_Ontology:HP:0004843,Human_Phenotype_Ontology:HP:0005516,Human_Phenotype_Ontology:HP:0006724,Human_Phenotype_Ontology:HP:0006728,MONDO:MONDO:0018874,MeSH:D015470,MedGen:C0023467,OMIM:601626,Orphanet:ORPHA519,SNOMED_CT:17788007|Human_Phenotype_Ontology:HP:0002861,Human_Phenotype_Ontology:HP:0002887,Human_Phenotype_Ontology:HP:0006777,Human_Phenotype_Ontology:HP:0007474,MONDO:MONDO:0005105,MeSH:D008545,MedGen:C0025202,SNOMED_CT:2092003,SNOMED_CT:372244006|Human_Phenotype_Ontology:HP:0002889,Human_Phenotype_Ontology:HP:0006744,Human_Phenotype_Ontology:HP:0006759,MeSH:D018268,MedGen:C0206686|Human_Phenotype_Ontology:HP:0003006,Human_Phenotype_Ontology:HP:0006738,MONDO:MONDO:0005072,MeSH:D009447,MedGen:C0027819,Orphanet:ORPHA635,SNOMED_CT:87364003|Human_Phenotype_Ontology:HP:0005550,Human_Phenotype_Ontology:HP:0006734,Human_Phenotype_Ontology:HP:0006760,MONDO:MONDO:0004948,MeSH:D015451,MedGen:C0023434,OMIM:151400,Orphanet:ORPHA67038,SNOMED_CT:277473004,SNOMED_CT:51092000|Human_Phenotype_Ontology:HP:0005600,Human_Phenotype_Ontology:HP:0005604,MONDO:MONDO:0044792,MedGen:C1842036,OMIM:137550,Orphanet:ORPHA626|Human_Phenotype_Ontology:HP:0006740,MONDO:MONDO:0005611,MedGen:C0279680|Human_Phenotype_Ontology:HP:0006775,MONDO:MONDO:0009693,MeSH:D009101,MedGen:C0026764,OMIM:254500,Orphanet:ORPHA29073,SNOMED_CT:109989006,SNOMED_CT:55921005|Human_Phenotype_Ontology:HP:0011797,MeSH:D002292,MedGen:C1336839,OMIM:605074|Human_Phenotype_Ontology:HP:0012056,MONDO:MONDO:0005012,MeSH:C562393,MedGen:C0151779,OMIM:PS155600,SNOMED_CT:93655004|Human_Phenotype_Ontology:HP:0030078,MONDO:MONDO:0005061,MeSH:C538231,MedGen:C0152013|Human_Phenotype_Ontology:HP:0030358,MONDO:MONDO:0005233,MeSH:D002289,MedGen:C0007131,SNOMED_CT:254637007|Human_Phenotype_Ontology:HP:0030692,MONDO:MONDO:0021211,MeSH:D001932,MedGen:C0006118,SNOMED_CT:126952004|Human_Phenotype_Ontology:HP:0100630,MONDO:MONDO:0005375,MeSH:D009303,MedGen:C0027439|Human_Phenotype_Ontology:HP:0100834,MeSH:D015179,MedGen:C0009404,SNOMED_CT:126837005|MONDO:MONDO:0005036,MedGen:C0278701|MONDO:MONDO:0006046,MedGen:C0279663|MONDO:MONDO:0009578,MedGen:C0544862,OMIM:249400,Orphanet:ORPHA2481|MONDO:MONDO:0018177,MeSH:D005909,MedGen:C0017636,Orphanet:ORPHA360,SNOMED_CT:63634009|MONDO:MONDO:0021060,MedGen:CN166718,Orphanet:ORPHA536391|MedGen:C0153574|MedGen:CN517202;CLNSIG=Conflicting_interpretations_of_pathogenicity;CLNHGVS=NC_000001.11:g.114713909G>T;GENEINFO=7989:4893;DPVID=2143;DPVSIG=Pathogenic;DPVDSDBID=OMIM:137550;DPVDBN=Spitz_nevus;DPVHGVS=NC_000001.11:g.114713909G>T	.