chr3-98532367-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_005290.4(GPR15):c.334A>G(p.Met112Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00401 in 1,614,134 control chromosomes in the GnomAD database, including 204 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 Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M112K) has been classified as Uncertain significance.
Frequency
Consequence
NM_005290.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPR15 | NM_005290.4 | c.334A>G | p.Met112Val | missense_variant | 1/1 | ENST00000284311.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPR15 | ENST00000284311.5 | c.334A>G | p.Met112Val | missense_variant | 1/1 | NM_005290.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0205 AC: 3113AN: 152132Hom.: 121 Cov.: 32
GnomAD3 exomes AF: 0.00560 AC: 1407AN: 251424Hom.: 32 AF XY: 0.00415 AC XY: 564AN XY: 135880
GnomAD4 exome AF: 0.00229 AC: 3345AN: 1461884Hom.: 83 Cov.: 34 AF XY: 0.00194 AC XY: 1414AN XY: 727244
GnomAD4 genome ? AF: 0.0205 AC: 3127AN: 152250Hom.: 121 Cov.: 32 AF XY: 0.0203 AC XY: 1509AN XY: 74422
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 25, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at