1-9104484-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_024980.5(GPR157):c.943G>A(p.Ala315Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000595 in 1,613,386 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A315E) has been classified as Uncertain significance.
Frequency
Consequence
NM_024980.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPR157 | NM_024980.5 | c.943G>A | p.Ala315Thr | missense_variant | 4/4 | ENST00000377411.5 | |
GPR157 | XM_005263496.6 | c.904G>A | p.Ala302Thr | missense_variant | 4/4 | ||
GPR157 | XM_005263497.6 | c.748G>A | p.Ala250Thr | missense_variant | 3/3 | ||
GPR157 | XR_007063977.1 | n.1018G>A | non_coding_transcript_exon_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPR157 | ENST00000377411.5 | c.943G>A | p.Ala315Thr | missense_variant | 4/4 | 1 | NM_024980.5 | P1 | |
GPR157 | ENST00000465853.1 | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000330 AC: 5AN: 151432Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000835 AC: 21AN: 251348Hom.: 1 AF XY: 0.0000883 AC XY: 12AN XY: 135828
GnomAD4 exome AF: 0.0000616 AC: 90AN: 1461836Hom.: 2 Cov.: 31 AF XY: 0.0000729 AC XY: 53AN XY: 727216
GnomAD4 genome AF: 0.0000396 AC: 6AN: 151550Hom.: 0 Cov.: 31 AF XY: 0.0000676 AC XY: 5AN XY: 74018
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 20, 2023 | The c.943G>A (p.A315T) alteration is located in exon 4 (coding exon 4) of the GPR157 gene. This alteration results from a G to A substitution at nucleotide position 943, causing the alanine (A) at amino acid position 315 to be replaced by a threonine (T). 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