rs2070025
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_021871.4(FGA):āc.16A>Gā(p.Ile6Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00281 in 1,557,848 control chromosomes in the GnomAD database, including 193 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_021871.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FGA | NM_021871.4 | c.16A>G | p.Ile6Val | missense_variant | 1/5 | ENST00000403106.8 | |
FGA | NM_000508.5 | c.16A>G | p.Ile6Val | missense_variant | 1/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FGA | ENST00000403106.8 | c.16A>G | p.Ile6Val | missense_variant | 1/5 | 1 | NM_021871.4 | ||
FGA | ENST00000651975.2 | c.16A>G | p.Ile6Val | missense_variant | 1/6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00349 AC: 531AN: 152214Hom.: 17 Cov.: 32
GnomAD3 exomes AF: 0.00764 AC: 1264AN: 165434Hom.: 51 AF XY: 0.00708 AC XY: 616AN XY: 87022
GnomAD4 exome AF: 0.00273 AC: 3837AN: 1405516Hom.: 176 Cov.: 30 AF XY: 0.00256 AC XY: 1775AN XY: 693736
GnomAD4 genome AF: 0.00351 AC: 534AN: 152332Hom.: 17 Cov.: 32 AF XY: 0.00400 AC XY: 298AN XY: 74488
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 05, 2021 | This variant is associated with the following publications: (PMID: 32877852) - |
Congenital afibrinogenemia Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Familial visceral amyloidosis, Ostertag type Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at