12-6823938-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_019858.2(GPR162):c.40C>A(p.Arg14Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000007 in 1,570,734 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 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. R14H) has been classified as Likely benign.
Frequency
Consequence
NM_019858.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPR162 | NM_019858.2 | c.40C>A | p.Arg14Ser | missense_variant | 2/5 | ENST00000311268.8 | |
GPR162 | NM_014449.2 | c.15+175C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPR162 | ENST00000311268.8 | c.40C>A | p.Arg14Ser | missense_variant | 2/5 | 1 | NM_019858.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152164Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000634 AC: 9AN: 1418570Hom.: 0 Cov.: 32 AF XY: 0.00000712 AC XY: 5AN XY: 701954
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152164Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 14, 2022 | The c.40C>A (p.R14S) alteration is located in exon 2 (coding exon 1) of the GPR162 gene. This alteration results from a C to A substitution at nucleotide position 40, causing the arginine (R) at amino acid position 14 to be replaced by a serine (S). 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