chr12-49041335-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2
The NM_003482.4(KMT2D):c.6435G>A(p.Pro2145Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000035 in 1,544,606 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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. P2145P) has been classified as Likely benign.
Frequency
Consequence
NM_003482.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000527 AC: 8AN: 151780Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000939 AC: 16AN: 170396Hom.: 0 AF XY: 0.0000867 AC XY: 8AN XY: 92256
GnomAD4 exome AF: 0.0000330 AC: 46AN: 1392710Hom.: 0 Cov.: 35 AF XY: 0.0000394 AC XY: 27AN XY: 686118
GnomAD4 genome AF: 0.0000527 AC: 8AN: 151896Hom.: 0 Cov.: 32 AF XY: 0.0000674 AC XY: 5AN XY: 74208
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
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Kabuki syndrome Benign:1
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KMT2D-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at