chr3-98532227-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_005290.4(GPR15):c.194G>A(p.Arg65Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00035 in 1,614,110 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005290.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPR15 | NM_005290.4 | c.194G>A | p.Arg65Gln | missense_variant | 1/1 | ENST00000284311.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPR15 | ENST00000284311.5 | c.194G>A | p.Arg65Gln | missense_variant | 1/1 | NM_005290.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000316 AC: 48AN: 152112Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000342 AC: 86AN: 251438Hom.: 1 AF XY: 0.000309 AC XY: 42AN XY: 135892
GnomAD4 exome AF: 0.000354 AC: 517AN: 1461880Hom.: 2 Cov.: 34 AF XY: 0.000323 AC XY: 235AN XY: 727238
GnomAD4 genome ? AF: 0.000315 AC: 48AN: 152230Hom.: 0 Cov.: 32 AF XY: 0.000363 AC XY: 27AN XY: 74434
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Oct 06, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at