2-1083646-G-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The ENST00000308624.10(SNTG2):āc.201G>Cā(p.Gln67His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000477 in 1,613,750 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
ENST00000308624.10 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SNTG2 | NM_018968.4 | c.201G>C | p.Gln67His | missense_variant | 2/17 | ENST00000308624.10 | NP_061841.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SNTG2 | ENST00000308624.10 | c.201G>C | p.Gln67His | missense_variant | 2/17 | 1 | NM_018968.4 | ENSP00000311837 | P1 | |
SNTG2 | ENST00000407292.1 | c.201G>C | p.Gln67His | missense_variant | 2/11 | 1 | ENSP00000385020 | |||
SNTG2 | ENST00000450962.5 | c.201G>C | p.Gln67His | missense_variant, NMD_transcript_variant | 2/8 | 5 | ENSP00000401997 | |||
SNTG2 | ENST00000452177.5 | c.201G>C | p.Gln67His | missense_variant, NMD_transcript_variant | 2/8 | 2 | ENSP00000412249 |
Frequencies
GnomAD3 genomes AF: 0.000197 AC: 30AN: 152212Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000482 AC: 12AN: 248944Hom.: 0 AF XY: 0.0000518 AC XY: 7AN XY: 135044
GnomAD4 exome AF: 0.0000322 AC: 47AN: 1461420Hom.: 0 Cov.: 33 AF XY: 0.0000303 AC XY: 22AN XY: 726996
GnomAD4 genome AF: 0.000197 AC: 30AN: 152330Hom.: 0 Cov.: 33 AF XY: 0.000215 AC XY: 16AN XY: 74508
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 06, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at