chr12-49051245-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_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 (★★).
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
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KMT2D | ENST00000301067.12 | c.2438C>T | p.Pro813Leu | missense_variant | Exon 11 of 55 | 5 | NM_003482.4 | ENSP00000301067.7 | ||
KMT2D | ENST00000683543.2 | c.2438C>T | p.Pro813Leu | missense_variant | Exon 11 of 56 | ENSP00000506726.1 | ||||
KMT2D | ENST00000685166.1 | c.2438C>T | p.Pro813Leu | missense_variant | Exon 10 of 54 | ENSP00000509386.1 | ||||
KMT2D | ENST00000692637.1 | c.2438C>T | p.Pro813Leu | missense_variant | Exon 10 of 54 | ENSP00000509666.1 |
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
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not provided Benign:3
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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