20-21161882-C-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_018474.6(KIZ):c.417C>G(p.His139Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.656 in 1,607,958 control chromosomes in the GnomAD database, including 352,336 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/13 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H139R) has been classified as Uncertain significance.
Frequency
Consequence
NM_018474.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.580 AC: 87862AN: 151470Hom.: 27079 Cov.: 30
GnomAD3 exomes AF: 0.646 AC: 160031AN: 247878Hom.: 53158 AF XY: 0.664 AC XY: 89208AN XY: 134412
GnomAD4 exome AF: 0.664 AC: 967574AN: 1456376Hom.: 325246 Cov.: 33 AF XY: 0.671 AC XY: 486456AN XY: 724726
GnomAD4 genome AF: 0.580 AC: 87914AN: 151582Hom.: 27090 Cov.: 30 AF XY: 0.585 AC XY: 43338AN XY: 74054
ClinVar
Submissions by phenotype
not provided Benign:2
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Retinal dystrophy Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at