12-118082364-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_019086.6(VSIG10):c.427G>A(p.Ala143Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000849 in 1,613,762 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_019086.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VSIG10 | NM_019086.6 | c.427G>A | p.Ala143Thr | missense_variant | 3/9 | ENST00000359236.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VSIG10 | ENST00000359236.10 | c.427G>A | p.Ala143Thr | missense_variant | 3/9 | 1 | NM_019086.6 | P1 | |
VSIG10 | ENST00000538357.1 | c.362-2758G>A | intron_variant | 2 | |||||
VSIG10 | ENST00000536905.5 | n.938G>A | non_coding_transcript_exon_variant | 4/4 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000125 AC: 19AN: 152088Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000565 AC: 14AN: 247946Hom.: 0 AF XY: 0.0000817 AC XY: 11AN XY: 134658
GnomAD4 exome AF: 0.0000807 AC: 118AN: 1461674Hom.: 0 Cov.: 32 AF XY: 0.0000729 AC XY: 53AN XY: 727128
GnomAD4 genome ? AF: 0.000125 AC: 19AN: 152088Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74294
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 01, 2022 | The c.427G>A (p.A143T) alteration is located in exon 3 (coding exon 3) of the VSIG10 gene. This alteration results from a G to A substitution at nucleotide position 427, causing the alanine (A) at amino acid position 143 to be replaced by a threonine (T). 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