chr15-101276643-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_018445.6(SELENOS):c.109A>G(p.Ile37Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000697 in 1,613,132 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018445.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SELENOS | NM_018445.6 | c.109A>G | p.Ile37Val | missense_variant | 2/6 | ENST00000526049.6 | |
SELENOS | NM_203472.3 | c.109A>G | p.Ile37Val | missense_variant | 2/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SELENOS | ENST00000526049.6 | c.109A>G | p.Ile37Val | missense_variant | 2/6 | 1 | NM_018445.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000513 AC: 78AN: 152074Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000471 AC: 117AN: 248458Hom.: 0 AF XY: 0.000438 AC XY: 59AN XY: 134850
GnomAD4 exome AF: 0.000716 AC: 1046AN: 1461058Hom.: 0 Cov.: 31 AF XY: 0.000684 AC XY: 497AN XY: 726804
GnomAD4 genome ? AF: 0.000513 AC: 78AN: 152074Hom.: 0 Cov.: 31 AF XY: 0.000458 AC XY: 34AN XY: 74272
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 07, 2022 | The c.109A>G (p.I37V) alteration is located in exon 2 (coding exon 2) of the VIMP gene. This alteration results from a A to G substitution at nucleotide position 109, causing the isoleucine (I) at amino acid position 37 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