chr12-6826831-A-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_019858.2(GPR162):c.1394A>C(p.Glu465Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000934 in 1,605,392 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E465K) has been classified 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.1394A>C | p.Glu465Ala | missense_variant | 5/5 | ENST00000311268.8 | |
GPR162 | NM_014449.2 | c.542A>C | p.Glu181Ala | missense_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPR162 | ENST00000311268.8 | c.1394A>C | p.Glu465Ala | missense_variant | 5/5 | 1 | NM_019858.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000198 AC: 3AN: 151644Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000162 AC: 4AN: 247644Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 133884
GnomAD4 exome AF: 0.00000826 AC: 12AN: 1453630Hom.: 0 Cov.: 33 AF XY: 0.0000111 AC XY: 8AN XY: 723048
GnomAD4 genome ? AF: 0.0000198 AC: 3AN: 151762Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74266
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 27, 2022 | The c.1394A>C (p.E465A) alteration is located in exon 5 (coding exon 4) of the GPR162 gene. This alteration results from a A to C substitution at nucleotide position 1394, causing the glutamic acid (E) at amino acid position 465 to be replaced by an alanine (A). 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