chr12-49033427-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_003482.4(KMT2D):c.11278G>A(p.Gly3760Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000019 in 1,581,650 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. G3760G) 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: 0.000113 AC: 17AN: 150288Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000451 AC: 9AN: 199398Hom.: 0 AF XY: 0.0000185 AC XY: 2AN XY: 107846
GnomAD4 exome AF: 0.00000908 AC: 13AN: 1431234Hom.: 0 Cov.: 48 AF XY: 0.00000705 AC XY: 5AN XY: 709516
GnomAD4 genome AF: 0.000113 AC: 17AN: 150416Hom.: 0 Cov.: 33 AF XY: 0.000122 AC XY: 9AN XY: 73506
ClinVar
Submissions by phenotype
not provided Uncertain:1
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not specified Benign:1
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Kabuki syndrome Benign:1
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Inborn genetic diseases Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at