rs2066865
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The 4-154604124-G-A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 414,858 control chromosomes in the GnomAD database, including 15,657 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.27 ( 5650 hom., cov: 32)
Exomes 𝑓: 0.26 ( 10007 hom. )
Consequence
FGG
NM_021870.3 downstream_gene
NM_021870.3 downstream_gene
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.104
Genes affected
FGG (HGNC:3694): (fibrinogen gamma chain) The protein encoded by this gene is the gamma component of fibrinogen, a blood-borne glycoprotein comprised of three pairs of nonidentical polypeptide chains. Following vascular injury, fibrinogen is cleaved by thrombin to form fibrin which is the most abundant component of blood clots. In addition, various cleavage products of fibrinogen and fibrin regulate cell adhesion and spreading, display vasoconstrictor and chemotactic activities, and are mitogens for several cell types. Mutations in this gene lead to several disorders, including dysfibrinogenemia, hypofibrinogenemia and thrombophilia. Alternative splicing results in transcript variants encoding different isoforms. [provided by RefSeq, Aug 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
?
Variant 4-154604124-G-A is Benign according to our data. Variant chr4-154604124-G-A is described in ClinVar as [Benign]. Clinvar id is 369438.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FGG | NM_021870.3 | downstream_gene_variant | ENST00000336098.8 | ||||
FGG | NM_000509.6 | downstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FGG | ENST00000336098.8 | downstream_gene_variant | 2 | NM_021870.3 |
Frequencies
GnomAD3 genomes ? AF: 0.266 AC: 40402AN: 151920Hom.: 5640 Cov.: 32
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GnomAD4 exome AF: 0.262 AC: 68902AN: 262820Hom.: 10007 Cov.: 4 AF XY: 0.261 AC XY: 34854AN XY: 133778
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GnomAD4 genome ? AF: 0.266 AC: 40446AN: 152038Hom.: 5650 Cov.: 32 AF XY: 0.268 AC XY: 19914AN XY: 74332
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Congenital afibrinogenemia Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 12, 2021 | This variant is associated with the following publications: (PMID: 31582554, 16144795, 17445871, 19492150, 17403086, 25772935) - |
Computational scores
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at