19-35718056-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_014727.3(KMT2B):c.38C>T(p.Pro13Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000405 in 986,818 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014727.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KMT2B | ENST00000420124.4 | c.38C>T | p.Pro13Leu | missense_variant | 1/37 | 1 | NM_014727.3 | ENSP00000398837.2 | ||
KMT2B | ENST00000673918.2 | c.38C>T | p.Pro13Leu | missense_variant | 1/37 | ENSP00000501283.1 | ||||
KMT2B | ENST00000687718.1 | n.38C>T | non_coding_transcript_exon_variant | 1/3 | ENSP00000510535.1 | |||||
KMT2B | ENST00000692961.1 | n.38C>T | non_coding_transcript_exon_variant | 1/36 | ENSP00000509289.1 |
Frequencies
GnomAD3 genomes AF: 0.00000682 AC: 1AN: 146606Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000357 AC: 3AN: 840212Hom.: 0 Cov.: 31 AF XY: 0.00000772 AC XY: 3AN XY: 388820
GnomAD4 genome AF: 0.00000682 AC: 1AN: 146606Hom.: 0 Cov.: 32 AF XY: 0.0000140 AC XY: 1AN XY: 71338
ClinVar
Submissions by phenotype
Dystonia 28, childhood-onset Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Department of Human Genetics, Hannover Medical School | Jan 17, 2025 | ACMG: PM2_Supporting, BP4 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at