9-133154199-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_021996.6(GBGT1):c.422G>A(p.Arg141Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000326 in 1,562,654 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_021996.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GBGT1 | ENST00000372040.9 | c.422G>A | p.Arg141Gln | missense_variant | Exon 7 of 7 | 1 | NM_021996.6 | ENSP00000361110.3 | ||
ENSG00000285245 | ENST00000647146.1 | c.396+979G>A | intron_variant | Intron 6 of 22 | ENSP00000493691.1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152146Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000109 AC: 24AN: 219984Hom.: 1 AF XY: 0.000101 AC XY: 12AN XY: 118308
GnomAD4 exome AF: 0.0000305 AC: 43AN: 1410390Hom.: 1 Cov.: 31 AF XY: 0.0000389 AC XY: 27AN XY: 694334
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152264Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74452
ClinVar
Submissions by phenotype
not specified Benign:1
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