NM_014373.3:c.64C>A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_014373.3(GPR160):c.64C>A(p.Leu22Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000832 in 1,578,902 control chromosomes in the GnomAD database, including 21 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_014373.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000618 AC: 94AN: 152156Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00171 AC: 384AN: 225036Hom.: 6 AF XY: 0.00243 AC XY: 296AN XY: 121758
GnomAD4 exome AF: 0.000854 AC: 1218AN: 1426628Hom.: 19 Cov.: 27 AF XY: 0.00124 AC XY: 882AN XY: 709148
GnomAD4 genome AF: 0.000624 AC: 95AN: 152274Hom.: 2 Cov.: 32 AF XY: 0.000873 AC XY: 65AN XY: 74446
ClinVar
Submissions by phenotype
GPR160-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at