12-49031240-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2
The NM_003482.4(KMT2D):c.13465G>A(p.Gly4489Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0000236 in 1,612,986 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar. Synonymous variant affecting the same amino acid position (i.e. G4489G) has been classified as Likely benign.
Frequency
Consequence
NM_003482.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152212Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000201 AC: 5AN: 248702Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134958
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1460656Hom.: 0 Cov.: 38 AF XY: 0.0000165 AC XY: 12AN XY: 726558
GnomAD4 genome AF: 0.0000919 AC: 14AN: 152330Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74482
ClinVar
Submissions by phenotype
not specified Uncertain:1
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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