22-46308717-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_016426.7(GTSE1):c.536G>A(p.Gly179Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000192 in 1,613,660 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_016426.7 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 |
---|---|---|---|---|---|---|---|
GTSE1 | NM_016426.7 | c.536G>A | p.Gly179Asp | missense_variant | 4/12 | ENST00000454366.2 | |
GTSE1 | XM_047441391.1 | c.536G>A | p.Gly179Asp | missense_variant | 3/11 | ||
GTSE1 | XM_047441392.1 | c.536G>A | p.Gly179Asp | missense_variant | 4/10 | ||
GTSE1 | XR_007067974.1 | n.619G>A | non_coding_transcript_exon_variant | 4/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GTSE1 | ENST00000454366.2 | c.536G>A | p.Gly179Asp | missense_variant | 4/12 | 1 | NM_016426.7 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152268Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000724 AC: 18AN: 248454Hom.: 0 AF XY: 0.0000519 AC XY: 7AN XY: 134930
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1461274Hom.: 0 Cov.: 33 AF XY: 0.0000124 AC XY: 9AN XY: 726904
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152386Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74514
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at