6-10529803-G-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 1P and 13B. PP3BP4_StrongBP6BS1BS2
The NM_145649.5(GCNT2):c.892G>A(p.Glu298Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000473 in 1,614,010 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_145649.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000618 AC: 94AN: 152148Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000909 AC: 228AN: 250874Hom.: 2 AF XY: 0.000892 AC XY: 121AN XY: 135596
GnomAD4 exome AF: 0.000458 AC: 670AN: 1461744Hom.: 3 Cov.: 32 AF XY: 0.000485 AC XY: 353AN XY: 727176
GnomAD4 genome AF: 0.000617 AC: 94AN: 152266Hom.: 0 Cov.: 32 AF XY: 0.000537 AC XY: 40AN XY: 74458
ClinVar
Submissions by phenotype
GCNT2-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). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at