rs2268574
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000162.5(GCK):c.679+38T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 1,592,566 control chromosomes in the GnomAD database, including 207,231 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_000162.5 intron
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: 0.570 AC: 86483AN: 151798Hom.: 25462 Cov.: 32
GnomAD3 exomes AF: 0.531 AC: 132823AN: 250270Hom.: 36046 AF XY: 0.518 AC XY: 70099AN XY: 135390
GnomAD4 exome AF: 0.499 AC: 718976AN: 1440652Hom.: 181745 Cov.: 26 AF XY: 0.496 AC XY: 356115AN XY: 717960
GnomAD4 genome AF: 0.570 AC: 86554AN: 151914Hom.: 25486 Cov.: 32 AF XY: 0.569 AC XY: 42208AN XY: 74226
ClinVar
Submissions by phenotype
not provided Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at