12-6826839-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_019858.2(GPR162):c.1402G>A(p.Glu468Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000484 in 1,611,402 control chromosomes in the GnomAD database, including 1 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_019858.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPR162 | NM_019858.2 | c.1402G>A | p.Glu468Lys | missense_variant | 5/5 | ENST00000311268.8 | |
GPR162 | NM_014449.2 | c.550G>A | p.Glu184Lys | missense_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPR162 | ENST00000311268.8 | c.1402G>A | p.Glu468Lys | missense_variant | 5/5 | 1 | NM_019858.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000788 AC: 12AN: 152216Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000805 AC: 20AN: 248510Hom.: 0 AF XY: 0.0000819 AC XY: 11AN XY: 134378
GnomAD4 exome AF: 0.0000452 AC: 66AN: 1459068Hom.: 1 Cov.: 33 AF XY: 0.0000482 AC XY: 35AN XY: 725736
GnomAD4 genome ? AF: 0.0000788 AC: 12AN: 152334Hom.: 0 Cov.: 31 AF XY: 0.0000403 AC XY: 3AN XY: 74478
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 22, 2022 | The c.1402G>A (p.E468K) alteration is located in exon 5 (coding exon 4) of the GPR162 gene. This alteration results from a G to A substitution at nucleotide position 1402, causing the glutamic acid (E) at amino acid position 468 to be replaced by a lysine (K). 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