3-151294753-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_023915.4(GPR87):c.493G>A(p.Val165Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00393 in 1,614,134 control chromosomes in the GnomAD database, including 16 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 Likely benign (★).
Frequency
Consequence
NM_023915.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GPR87 | ENST00000260843.5 | c.493G>A | p.Val165Ile | missense_variant | Exon 3 of 3 | 1 | NM_023915.4 | ENSP00000260843.4 | ||
MED12L | ENST00000687756.1 | c.2251-55306C>T | intron_variant | Intron 16 of 44 | NM_001393769.1 | ENSP00000508695.1 |
Frequencies
GnomAD3 genomes AF: 0.00223 AC: 340AN: 152176Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00240 AC: 603AN: 251292Hom.: 4 AF XY: 0.00242 AC XY: 328AN XY: 135800
GnomAD4 exome AF: 0.00410 AC: 5999AN: 1461840Hom.: 15 Cov.: 34 AF XY: 0.00391 AC XY: 2844AN XY: 727226
GnomAD4 genome AF: 0.00223 AC: 340AN: 152294Hom.: 1 Cov.: 32 AF XY: 0.00203 AC XY: 151AN XY: 74468
ClinVar
Submissions by phenotype
not provided Benign:1
ENSG00000286273: BS2; GPR87: BP4, BS2; MED12L: BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at