chr1-9104633-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_024980.5(GPR157):c.794G>A(p.Gly265Asp) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.00000314 in 1,589,972 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024980.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPR157 | NM_024980.5 | c.794G>A | p.Gly265Asp | missense_variant, splice_region_variant | 4/4 | ENST00000377411.5 | |
GPR157 | XM_005263496.6 | c.755G>A | p.Gly252Asp | missense_variant, splice_region_variant | 4/4 | ||
GPR157 | XM_005263497.6 | c.599G>A | p.Gly200Asp | missense_variant, splice_region_variant | 3/3 | ||
GPR157 | XR_007063977.1 | n.869G>A | splice_region_variant, non_coding_transcript_exon_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPR157 | ENST00000377411.5 | c.794G>A | p.Gly265Asp | missense_variant, splice_region_variant | 4/4 | 1 | NM_024980.5 | P1 | |
GPR157 | ENST00000465853.1 | c.98G>A | p.Gly33Asp | missense_variant, splice_region_variant | 2/2 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152022Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000137 AC: 3AN: 218714Hom.: 0 AF XY: 0.0000169 AC XY: 2AN XY: 118046
GnomAD4 exome AF: 0.00000278 AC: 4AN: 1437950Hom.: 0 Cov.: 30 AF XY: 0.00000421 AC XY: 3AN XY: 712744
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152022Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74234
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at