X-108076209-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_182607.5(VSIG1):c.821C>T(p.Ala274Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000415 in 1,206,229 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/20 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.821C>T | p.Ala274Val | missense_variant | Exon 6 of 7 | 1 | NM_182607.5 | ENSP00000217957.3 | ||
VSIG1 | ENST00000415430.7 | c.929C>T | p.Ala310Val | missense_variant | Exon 7 of 8 | 2 | ENSP00000402219.3 |
Frequencies
GnomAD3 genomes AF: 0.0000178 AC: 2AN: 112095Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34257
GnomAD4 exome AF: 0.00000274 AC: 3AN: 1094134Hom.: 0 Cov.: 30 AF XY: 0.00000556 AC XY: 2AN XY: 359728
GnomAD4 genome AF: 0.0000178 AC: 2AN: 112095Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34257
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.929C>T (p.A310V) alteration is located in exon 7 (coding exon 7) of the VSIG1 gene. This alteration results from a C to T substitution at nucleotide position 929, causing the alanine (A) at amino acid position 310 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