chr12-49033482-TTGC-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 0P and 3B. BP3BP6_Moderate
The NM_003482.4(KMT2D):c.11220_11222del(p.Gln3745del) variant causes a inframe deletion change. The variant allele was found at a frequency of 0.0000205 in 1,609,696 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000022 ( 0 hom. )
Consequence
KMT2D
NM_003482.4 inframe_deletion
NM_003482.4 inframe_deletion
Scores
Not classified
Clinical Significance
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 -3 ACMG points.
BP3
?
Nonframeshift variant in repetitive region in NM_003482.4
BP6
?
Variant 12-49033482-TTGC-T is Benign according to our data. Variant chr12-49033482-TTGC-T is described in ClinVar as [Likely_benign]. Clinvar id is 3038831.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-49033482-TTGC-T is described in Lovd as [Likely_benign].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KMT2D | NM_003482.4 | c.11220_11222del | p.Gln3745del | inframe_deletion | 40/55 | ENST00000301067.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KMT2D | ENST00000301067.12 | c.11220_11222del | p.Gln3745del | inframe_deletion | 40/55 | 5 | NM_003482.4 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000659 AC: 1AN: 151750Hom.: 0 Cov.: 33
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GnomAD4 exome AF: 0.0000219 AC: 32AN: 1457946Hom.: 0 AF XY: 0.0000290 AC XY: 21AN XY: 725278
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
KMT2D-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 08, 2020 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at