rs148688181
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2
The NM_003482.4(KMT2D):c.10233C>T(p.Asp3411Asp) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00142 in 1,613,976 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_003482.4 splice_region, 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: 0.00103 AC: 157AN: 152206Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000955 AC: 238AN: 249194Hom.: 0 AF XY: 0.000939 AC XY: 127AN XY: 135206
GnomAD4 exome AF: 0.00146 AC: 2138AN: 1461652Hom.: 3 Cov.: 33 AF XY: 0.00138 AC XY: 1000AN XY: 727090
GnomAD4 genome AF: 0.00103 AC: 157AN: 152324Hom.: 0 Cov.: 32 AF XY: 0.000953 AC XY: 71AN XY: 74466
ClinVar
Submissions by phenotype
not specified Benign:4
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Kabuki syndrome 1 Uncertain:1Benign:1
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not provided Benign:2
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KMT2D: BP4, BP7, BS1 -
Kabuki syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at