chr3-170084471-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_014373.3(GPR160):c.499C>A(p.Gln167Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000144 in 1,461,386 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014373.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GPR160 | ENST00000355897.10 | c.499C>A | p.Gln167Lys | missense_variant | Exon 4 of 4 | 1 | NM_014373.3 | ENSP00000348161.5 | ||
GPR160 | ENST00000485735.6 | c.*10C>A | downstream_gene_variant | 2 | ENSP00000419546.2 | |||||
GPR160 | ENST00000473675.1 | c.*68C>A | downstream_gene_variant | 3 | ENSP00000420751.1 | |||||
GPR160 | ENST00000482710.1 | c.*234C>A | downstream_gene_variant | 2 | ENSP00000419400.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 250704Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135478
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461386Hom.: 0 Cov.: 30 AF XY: 0.0000110 AC XY: 8AN XY: 727002
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.499C>A (p.Q167K) alteration is located in exon 4 (coding exon 1) of the GPR160 gene. This alteration results from a C to A substitution at nucleotide position 499, causing the glutamine (Q) at amino acid position 167 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