rs2066874
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PP3_ModerateBS1BS2
The NM_021870.3(FGG):c.851+37A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00164 in 1,599,256 control chromosomes in the GnomAD database, including 34 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0088 ( 22 hom., cov: 32)
Exomes 𝑓: 0.00089 ( 12 hom. )
Consequence
FGG
NM_021870.3 intron
NM_021870.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.427
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 Likely_benign. Variant got -6 ACMG points.
PP3
?
Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00878 (1337/152302) while in subpopulation AFR AF= 0.0308 (1282/41570). AF 95% confidence interval is 0.0294. There are 22 homozygotes in gnomad4. There are 617 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 22 SD gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FGG | NM_021870.3 | c.851+37A>G | intron_variant | ENST00000336098.8 | |||
FGG | NM_000509.6 | c.851+37A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FGG | ENST00000336098.8 | c.851+37A>G | intron_variant | 2 | NM_021870.3 |
Frequencies
GnomAD3 genomes ? AF: 0.00880 AC: 1339AN: 152184Hom.: 22 Cov.: 32
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GnomAD3 exomes AF: 0.00245 AC: 581AN: 237308Hom.: 10 AF XY: 0.00176 AC XY: 226AN XY: 128248
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GnomAD4 exome AF: 0.000886 AC: 1282AN: 1446954Hom.: 12 Cov.: 30 AF XY: 0.000784 AC XY: 564AN XY: 719476
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GnomAD4 genome ? AF: 0.00878 AC: 1337AN: 152302Hom.: 22 Cov.: 32 AF XY: 0.00828 AC XY: 617AN XY: 74474
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
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Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AG_spliceai
Position offset: -1
Find out detailed SpliceAI scores and Pangolin per-transcript scores at