chr12-49052257-C-T
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBA1
The NM_003482.4(KMT2D):c.1426G>A(p.Ala476Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.018 in 1,478,052 control chromosomes in the GnomAD database, including 3,260 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 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 -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KMT2D | NM_003482.4 | c.1426G>A | p.Ala476Thr | missense_variant | 11/55 | ENST00000301067.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KMT2D | ENST00000301067.12 | c.1426G>A | p.Ala476Thr | missense_variant | 11/55 | 5 | NM_003482.4 | A2 | |
KMT2D | ENST00000683543.2 | c.1426G>A | p.Ala476Thr | missense_variant | 11/56 | P4 | |||
KMT2D | ENST00000685166.1 | c.1426G>A | p.Ala476Thr | missense_variant | 10/54 | A2 | |||
KMT2D | ENST00000692637.1 | c.1426G>A | p.Ala476Thr | missense_variant | 10/54 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0888 AC: 12313AN: 138598Hom.: 1636 Cov.: 30
GnomAD3 exomes AF: 0.0277 AC: 5707AN: 205848Hom.: 677 AF XY: 0.0217 AC XY: 2447AN XY: 112910
GnomAD4 exome AF: 0.0107 AC: 14277AN: 1339318Hom.: 1610 Cov.: 37 AF XY: 0.00982 AC XY: 6494AN XY: 661574
GnomAD4 genome AF: 0.0892 AC: 12373AN: 138734Hom.: 1650 Cov.: 30 AF XY: 0.0860 AC XY: 5802AN XY: 67490
ClinVar
Submissions by phenotype
not specified Benign:3Other:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Feb 08, 2013 | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Mar 16, 2016 | - - |
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Kabuki syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Kabuki syndrome 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Sep 20, 2018 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at