rs144376311
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PP2BP4_StrongBP6_ModerateBS2
The NM_170606.3(KMT2C):c.10024G>T(p.Ala3342Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000416 in 1,609,114 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_170606.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KMT2C | NM_170606.3 | c.10024G>T | p.Ala3342Ser | missense_variant | 43/59 | ENST00000262189.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KMT2C | ENST00000262189.11 | c.10024G>T | p.Ala3342Ser | missense_variant | 43/59 | 1 | NM_170606.3 | P2 |
Frequencies
GnomAD3 genomes AF: 0.000243 AC: 37AN: 152084Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000564 AC: 14AN: 248142Hom.: 0 AF XY: 0.0000448 AC XY: 6AN XY: 133960
GnomAD4 exome AF: 0.0000206 AC: 30AN: 1456912Hom.: 0 Cov.: 33 AF XY: 0.0000166 AC XY: 12AN XY: 724140
GnomAD4 genome AF: 0.000243 AC: 37AN: 152202Hom.: 0 Cov.: 32 AF XY: 0.000296 AC XY: 22AN XY: 74414
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | May 20, 2023 | - - |
not specified Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at