rs774164988
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_003482.4(KMT2D):c.6477C>T(p.Leu2159=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000833 in 1,525,482 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. L2159L) 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 -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KMT2D | NM_003482.4 | c.6477C>T | p.Leu2159= | synonymous_variant | 32/55 | ENST00000301067.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KMT2D | ENST00000301067.12 | c.6477C>T | p.Leu2159= | synonymous_variant | 32/55 | 5 | NM_003482.4 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152044Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000518 AC: 8AN: 154302Hom.: 0 AF XY: 0.0000601 AC XY: 5AN XY: 83144
GnomAD4 exome AF: 0.0000837 AC: 115AN: 1373438Hom.: 0 Cov.: 35 AF XY: 0.0000682 AC XY: 46AN XY: 674966
GnomAD4 genome AF: 0.0000789 AC: 12AN: 152044Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74244
ClinVar
Submissions by phenotype
Kabuki syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 06, 2022 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jun 20, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at