rs80132640
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_003482.4(KMT2D):c.12028T>C(p.Ser4010Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0275 in 1,613,664 control chromosomes in the GnomAD database, including 744 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_003482.4 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: 0.0245 AC: 3723AN: 152034Hom.: 74 Cov.: 33
GnomAD3 exomes AF: 0.0263 AC: 6520AN: 248348Hom.: 102 AF XY: 0.0267 AC XY: 3601AN XY: 134948
GnomAD4 exome AF: 0.0279 AC: 40721AN: 1461510Hom.: 670 Cov.: 52 AF XY: 0.0278 AC XY: 20239AN XY: 727012
GnomAD4 genome AF: 0.0245 AC: 3723AN: 152154Hom.: 74 Cov.: 33 AF XY: 0.0246 AC XY: 1831AN XY: 74388
ClinVar
Submissions by phenotype
not specified Benign:6Other:1
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not provided Benign:4
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Kabuki syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at