rs75226229
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBA1
The NM_003482.4(KMT2D):c.2438C>T(p.Pro813Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0502 in 1,534,894 control chromosomes in the GnomAD database, including 2,365 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 (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P813R) has been classified as Uncertain significance.
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.2438C>T | p.Pro813Leu | missense_variant | 11/55 | ENST00000301067.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KMT2D | ENST00000301067.12 | c.2438C>T | p.Pro813Leu | missense_variant | 11/55 | 5 | NM_003482.4 | A2 | |
KMT2D | ENST00000683543.2 | c.2438C>T | p.Pro813Leu | missense_variant | 11/56 | P4 | |||
KMT2D | ENST00000685166.1 | c.2438C>T | p.Pro813Leu | missense_variant | 10/54 | A2 | |||
KMT2D | ENST00000692637.1 | c.2438C>T | p.Pro813Leu | missense_variant | 10/54 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0417 AC: 6300AN: 151202Hom.: 202 Cov.: 28
GnomAD3 exomes AF: 0.0420 AC: 7835AN: 186726Hom.: 264 AF XY: 0.0426 AC XY: 4263AN XY: 100022
GnomAD4 exome AF: 0.0511 AC: 70729AN: 1383574Hom.: 2163 Cov.: 34 AF XY: 0.0503 AC XY: 34266AN XY: 681452
GnomAD4 genome ? AF: 0.0416 AC: 6299AN: 151320Hom.: 202 Cov.: 28 AF XY: 0.0426 AC XY: 3149AN XY: 73916
ClinVar
Submissions by phenotype
not specified Benign:3Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 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 02, 2016 | - - |
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Feb 08, 2013 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Aug 28, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Kabuki syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at