12-49049775-T-C
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_003482.4(KMT2D):c.3813A>G(p.Leu1271=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,362 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. L1271L) has been classified as Likely benign.
Frequency
Consequence
NM_003482.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KMT2D | NM_003482.4 | c.3813A>G | p.Leu1271= | synonymous_variant | 12/55 | ENST00000301067.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KMT2D | ENST00000301067.12 | c.3813A>G | p.Leu1271= | synonymous_variant | 12/55 | 5 | NM_003482.4 | A2 | |
KMT2D | ENST00000683543.2 | c.3813A>G | p.Leu1271= | synonymous_variant | 12/56 | P4 | |||
KMT2D | ENST00000685166.1 | c.3813A>G | p.Leu1271= | synonymous_variant | 11/54 | A2 | |||
KMT2D | ENST00000692637.1 | c.3813A>G | p.Leu1271= | synonymous_variant | 11/54 | A2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 249044Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135106
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461362Hom.: 0 Cov.: 34 AF XY: 0.00000275 AC XY: 2AN XY: 726904
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Dec 12, 2014 | - - |
Kabuki syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at