12-6826867-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_019858.2(GPR162):c.1430C>T(p.Ala477Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000459 in 1,612,800 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPR162 | NM_019858.2 | c.1430C>T | p.Ala477Val | missense_variant | 5/5 | ENST00000311268.8 | |
GPR162 | NM_014449.2 | c.578C>T | p.Ala193Val | missense_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPR162 | ENST00000311268.8 | c.1430C>T | p.Ala477Val | missense_variant | 5/5 | 1 | NM_019858.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152204Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000441 AC: 11AN: 249552Hom.: 0 AF XY: 0.0000815 AC XY: 11AN XY: 134980
GnomAD4 exome AF: 0.0000479 AC: 70AN: 1460478Hom.: 1 Cov.: 33 AF XY: 0.0000619 AC XY: 45AN XY: 726446
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152322Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74486
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 01, 2021 | The c.1430C>T (p.A477V) alteration is located in exon 5 (coding exon 4) of the GPR162 gene. This alteration results from a C to T substitution at nucleotide position 1430, causing the alanine (A) at amino acid position 477 to be replaced by a valine (V). 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