12-49033482-TTGCTGCTGCTGC-TTGCTGCTGCTGCTGCTGC
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP3BS2
The NM_003482.4(KMT2D):c.11222_11223insGCAGCA(p.Gln3744_Gln3745dup) variant causes a inframe insertion change. The variant allele was found at a frequency of 0.00000683 in 1,611,218 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000069 ( 0 hom. )
Consequence
KMT2D
NM_003482.4 inframe_insertion
NM_003482.4 inframe_insertion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.57
Genes affected
KMT2D (HGNC:7133): (lysine methyltransferase 2D) The protein encoded by this gene is a histone methyltransferase that methylates the Lys-4 position of histone H3. The encoded protein is part of a large protein complex called ASCOM, which has been shown to be a transcriptional regulator of the beta-globin and estrogen receptor genes. Mutations in this gene have been shown to be a cause of Kabuki syndrome. [provided by RefSeq, Oct 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP3
Nonframeshift variant in repetitive region in NM_003482.4
BS2
High AC in GnomAdExome4 at 10 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KMT2D | NM_003482.4 | c.11222_11223insGCAGCA | p.Gln3744_Gln3745dup | inframe_insertion | 40/55 | ENST00000301067.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KMT2D | ENST00000301067.12 | c.11222_11223insGCAGCA | p.Gln3744_Gln3745dup | inframe_insertion | 40/55 | 5 | NM_003482.4 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00000659 AC: 1AN: 151764Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000171 AC: 4AN: 233912Hom.: 0 AF XY: 0.0000236 AC XY: 3AN XY: 127272
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GnomAD4 exome AF: 0.00000685 AC: 10AN: 1459454Hom.: 0 Cov.: 47 AF XY: 0.00000689 AC XY: 5AN XY: 726018
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GnomAD4 genome AF: 0.00000659 AC: 1AN: 151764Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74130
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at