X-108077268-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_182607.5(VSIG1):c.1051G>A(p.Glu351Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000043 in 1,210,346 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 16 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 (★).
Frequency
Consequence
NM_182607.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VSIG1 | ENST00000217957.10 | c.1051G>A | p.Glu351Lys | missense_variant | Exon 7 of 7 | 1 | NM_182607.5 | ENSP00000217957.3 | ||
VSIG1 | ENST00000415430.7 | c.1159G>A | p.Glu387Lys | missense_variant | Exon 8 of 8 | 2 | ENSP00000402219.3 |
Frequencies
GnomAD3 genomes AF: 0.0000268 AC: 3AN: 112089Hom.: 0 Cov.: 23 AF XY: 0.0000292 AC XY: 1AN XY: 34243
GnomAD3 exomes AF: 0.0000109 AC: 2AN: 183344Hom.: 0 AF XY: 0.0000147 AC XY: 1AN XY: 67820
GnomAD4 exome AF: 0.0000446 AC: 49AN: 1098257Hom.: 0 Cov.: 31 AF XY: 0.0000413 AC XY: 15AN XY: 363611
GnomAD4 genome AF: 0.0000268 AC: 3AN: 112089Hom.: 0 Cov.: 23 AF XY: 0.0000292 AC XY: 1AN XY: 34243
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1159G>A (p.E387K) alteration is located in exon 8 (coding exon 8) of the VSIG1 gene. This alteration results from a G to A substitution at nucleotide position 1159, causing the glutamic acid (E) at amino acid position 387 to be replaced by a lysine (K). 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