Variant Detail

Variant Information
ID
DPV: 8475
Chromosome
15
Gene
HGVS (GRCh37/hg19)
NC_000015.9:g.48738898C>T
HGVS (GRCh38/hg38)
NC_000015.10:g.48446701C>T
HGVS (RNA)
NM_000138.4:c.5788+5G>A
HGVS (Protein)
dbSNP
-
ClinGen Allele Registry
CA016065
Allele Frequency
Individual Information

ID
DPVS:8799.1
Clinical Significance
Pathogenic
Date Last Evaluated
2019-03-29
Clinical Significance Citation
Takeda, N. Impact of Pathogenic FBN1 Variant Types on the Progression of Aortic Disease in Patients With Marfan Syndrome. 2018 Circ Genom Precis Med. 2018 Jun;11(6):e002058. doi: 10.1161/CIRCGEN.117.002058. PMID:29848614
Sakai, H. Comprehensive genetic analysis of relevant four genes in 49 patients with Marfan syndrome or Marfan-related phenotypes. 2006 Am J Med Genet A. 2006 Aug 15;140(16):1719-25. doi: 10.1002/ajmg.a.31353. PMID:16835936

Transcript
-
Disease

Phenotype
-
Zygosity
single heterozygote
Allele Origin
unknown
Affected Status
yes
Sample Type
  • DNA
Analysis Type
  • SEQuencing
Collection Method
literature only
Compound heterozygous variant(s)
Data Submitter
Comment
Exon 47 deletion

ClinVar
Model Animals
VCF
VCF (GRCh37/hg19) 
											##fileformat=VCFv4.0
##reference=GRCh37
##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=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
15	48738898	NC_000015.9:g.48738898C>T	C	T	.	.	GNOMAD_AF=0;GNOMAD_AC=0;GNOMAD_AN=251014;CLNALLELEID=51564;CLNDN=Severe_Myopia|Ectopia_lentis|Arachnodactyly|Ischemic_stroke,_susceptibility_to|Aortic_root_dilatation|Dissecting_aortic_dilatation|Melanoma|Marfan_syndrome|Familial_thoracic_aortic_aneurysm_and_aortic_dissection|Marfan_Syndrome/Loeys-Dietz_Syndrome/Familial_Thoracic_Aortic_Aneurysms_and_Dissections|not_provided;CLNDISDB=Human_Phenotype_Ontology:HP:0000569,Human_Phenotype_Ontology:HP:0011003,MedGen:C0271183|Human_Phenotype_Ontology:HP:0000665,Human_Phenotype_Ontology:HP:0001083,Human_Phenotype_Ontology:HP:0007637,Human_Phenotype_Ontology:HP:0007882,Human_Phenotype_Ontology:HP:0008016,MedGen:C0013581,SNOMED_CT:74969002|Human_Phenotype_Ontology:HP:0001166,Human_Phenotype_Ontology:HP:0001505,MedGen:C0003706|Human_Phenotype_Ontology:HP:0002140,MONDO:MONDO:0020671,MedGen:C0948008,OMIM:601367,SNOMED_CT:422504002|Human_Phenotype_Ontology:HP:0002616,Human_Phenotype_Ontology:HP:0004750,Human_Phenotype_Ontology:HP:0005125,MedGen:C0238669|Human_Phenotype_Ontology:HP:0002622,MedGen:C0012736|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|MONDO:MONDO:0007947,MedGen:C0024796,OMIM:154700,Orphanet:ORPHA284963,Orphanet:ORPHA558,SNOMED_CT:19346006|MONDO:MONDO:0019625,MedGen:C4707243,OMIM:PS607086,Orphanet:ORPHA91387|MedGen:CN229799|MedGen:CN517202;CLNSIG=Pathogenic;CLNHGVS=NC_000015.9:g.48738898C>T;GENEINFO=3603:2200;DPVID=8475;DPVSIG=Pathogenic;DPVDSDBID=OMIM:154700;DPVDBN=Marfan_syndrome;DPVHGVS=NC_000015.9:g.48738898C>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-mhj96jx5>
##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
15	48446701	NC_000015.9:g.48738898C>T	C	T	.	.	dbSNP_RSID=rs193922219;GNOMAD_AF=0;GNOMAD_AC=0;GNOMAD_AN=251014;CLNALLELEID=51564;CLNDN=Severe_Myopia|Ectopia_lentis|Arachnodactyly|Ischemic_stroke|Aortic_root_dilatation|Dissecting_aortic_dilatation|Melanoma|Marfan_syndrome|Familial_thoracic_aortic_aneurysm_and_aortic_dissection|Marfan_Syndrome/Loeys-Dietz_Syndrome/Familial_Thoracic_Aortic_Aneurysms_and_Dissections|not_provided;CLNDISDB=Human_Phenotype_Ontology:HP:0000569,Human_Phenotype_Ontology:HP:0011003,MedGen:C0271183|Human_Phenotype_Ontology:HP:0000665,Human_Phenotype_Ontology:HP:0001083,Human_Phenotype_Ontology:HP:0007637,Human_Phenotype_Ontology:HP:0007882,Human_Phenotype_Ontology:HP:0008016,MedGen:C0013581,Orphanet:ORPHA1885,SNOMED_CT:74969002|Human_Phenotype_Ontology:HP:0001166,Human_Phenotype_Ontology:HP:0001505,MedGen:C0003706|Human_Phenotype_Ontology:HP:0002140,MedGen:C0948008,OMIM:601367,SNOMED_CT:422504002|Human_Phenotype_Ontology:HP:0002616,Human_Phenotype_Ontology:HP:0004750,Human_Phenotype_Ontology:HP:0005125,MedGen:C1298820|Human_Phenotype_Ontology:HP:0002622,MedGen:C0012736|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|MONDO:MONDO:0007947,MedGen:C0024796,OMIM:154700,Orphanet:ORPHA284963,Orphanet:ORPHA558,SNOMED_CT:19346006|MONDO:MONDO:0019625,MedGen:C4707243,OMIM:PS607086,Orphanet:ORPHA91387|MedGen:CN229799|MedGen:CN517202;CLNSIG=Pathogenic;CLNHGVS=NC_000015.10:g.48446701C>T;GENEINFO=3603:2200;DPVID=8475;DPVSIG=Pathogenic;DPVDSDBID=OMIM:154700;DPVDBN=Marfan_syndrome;DPVHGVS=NC_000015.10:g.48446701C>T	.