rs1555138529
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_001197104.2(KMT2A):c.134del(p.Pro45ArgfsTer105) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000345 in 1,158,230 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. P44P) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001197104.2 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KMT2A | NM_001197104.2 | c.134del | p.Pro45ArgfsTer105 | frameshift_variant | 1/36 | ENST00000534358.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KMT2A | ENST00000534358.8 | c.134del | p.Pro45ArgfsTer105 | frameshift_variant | 1/36 | 1 | NM_001197104.2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00000672 AC: 1AN: 148872Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000297 AC: 3AN: 1009358Hom.: 0 Cov.: 24 AF XY: 0.00000419 AC XY: 2AN XY: 477810
GnomAD4 genome ? AF: 0.00000672 AC: 1AN: 148872Hom.: 0 Cov.: 32 AF XY: 0.0000138 AC XY: 1AN XY: 72594
ClinVar
Submissions by phenotype
Inborn genetic diseases Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 18, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at