chr3-134604001-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_178554.6(KY):c.1564G>A(p.Glu522Lys) variant causes a missense change. The variant allele was found at a frequency of 0.000277 in 1,613,752 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_178554.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000276 AC: 42AN: 152226Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000554 AC: 138AN: 249082Hom.: 1 AF XY: 0.000518 AC XY: 70AN XY: 135120
GnomAD4 exome AF: 0.000277 AC: 405AN: 1461526Hom.: 2 Cov.: 70 AF XY: 0.000261 AC XY: 190AN XY: 727024
GnomAD4 genome AF: 0.000276 AC: 42AN: 152226Hom.: 0 Cov.: 33 AF XY: 0.000403 AC XY: 30AN XY: 74360
ClinVar
Submissions by phenotype
KY-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at