6-167157252-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_005299.3(GPR31):c.580G>A(p.Val194Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000229 in 1,614,026 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005299.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GPR31 | ENST00000366834.2 | c.580G>A | p.Val194Met | missense_variant | Exon 1 of 1 | 6 | NM_005299.3 | ENSP00000355799.2 | ||
ENSG00000291286 | ENST00000486697.2 | n.123-7149C>T | intron_variant | Intron 2 of 3 | 5 | |||||
ENSG00000291286 | ENST00000539001.6 | n.369-7149C>T | intron_variant | Intron 2 of 4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152164Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251380Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135870
GnomAD4 exome AF: 0.0000219 AC: 32AN: 1461862Hom.: 0 Cov.: 31 AF XY: 0.0000234 AC XY: 17AN XY: 727236
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152164Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.580G>A (p.V194M) alteration is located in exon 1 (coding exon 1) of the GPR31 gene. This alteration results from a G to A substitution at nucleotide position 580, causing the valine (V) at amino acid position 194 to be replaced by a methionine (M). 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