X-108061509-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_001170553.2(VSIG1):c.295C>T(p.Arg99Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,164,527 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 10/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001170553.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VSIG1 | NM_182607.5 | c.213+3308C>T | intron_variant | ENST00000217957.10 | NP_872413.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VSIG1 | ENST00000217957.10 | c.213+3308C>T | intron_variant | 1 | NM_182607.5 | ENSP00000217957.3 | ||||
VSIG1 | ENST00000415430.7 | c.295C>T | p.Arg99Trp | missense_variant | 3/8 | 2 | ENSP00000402219.3 | |||
VSIG1 | ENST00000458383.1 | c.295C>T | p.Arg99Trp | missense_variant | 3/4 | 4 | ENSP00000407102.1 |
Frequencies
GnomAD3 genomes AF: 0.00000900 AC: 1AN: 111172Hom.: 0 Cov.: 22 AF XY: 0.0000299 AC XY: 1AN XY: 33420
GnomAD4 exome AF: 0.0000114 AC: 12AN: 1053355Hom.: 0 Cov.: 29 AF XY: 0.00000871 AC XY: 3AN XY: 344251
GnomAD4 genome AF: 0.00000900 AC: 1AN: 111172Hom.: 0 Cov.: 22 AF XY: 0.0000299 AC XY: 1AN XY: 33420
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 25, 2023 | The c.295C>T (p.R99W) alteration is located in exon 3 (coding exon 3) of the VSIG1 gene. This alteration results from a C to T substitution at nucleotide position 295, causing the arginine (R) at amino acid position 99 to be replaced by a tryptophan (W). 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