X-108058064-A-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_182607.5(VSIG1):āc.76A>Gā(p.Ile26Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000019 in 1,208,402 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 10 hemizygotes in GnomAD. 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 Uncertain significance (ā ).
Frequency
Consequence
NM_182607.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VSIG1 | ENST00000217957.10 | c.76A>G | p.Ile26Val | missense_variant | Exon 2 of 7 | 1 | NM_182607.5 | ENSP00000217957.3 | ||
VSIG1 | ENST00000415430.7 | c.76A>G | p.Ile26Val | missense_variant | Exon 2 of 8 | 2 | ENSP00000402219.3 | |||
VSIG1 | ENST00000458383.1 | c.76A>G | p.Ile26Val | missense_variant | Exon 2 of 4 | 4 | ENSP00000407102.1 |
Frequencies
GnomAD3 genomes AF: 0.0000897 AC: 10AN: 111448Hom.: 0 Cov.: 23 AF XY: 0.000149 AC XY: 5AN XY: 33648
GnomAD3 exomes AF: 0.0000497 AC: 9AN: 180967Hom.: 0 AF XY: 0.0000457 AC XY: 3AN XY: 65665
GnomAD4 exome AF: 0.0000119 AC: 13AN: 1096902Hom.: 0 Cov.: 30 AF XY: 0.0000138 AC XY: 5AN XY: 362566
GnomAD4 genome AF: 0.0000897 AC: 10AN: 111500Hom.: 0 Cov.: 23 AF XY: 0.000148 AC XY: 5AN XY: 33710
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.76A>G (p.I26V) alteration is located in exon 2 (coding exon 2) of the VSIG1 gene. This alteration results from a A to G substitution at nucleotide position 76, causing the isoleucine (I) at amino acid position 26 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at