rs145650484
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP6BS1BS2
The NM_014159.7(SETD2):āc.1885A>Gā(p.Lys629Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00062 in 1,610,826 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_014159.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000440 AC: 67AN: 152224Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000297 AC: 73AN: 245382Hom.: 0 AF XY: 0.000315 AC XY: 42AN XY: 133128
GnomAD4 exome AF: 0.000638 AC: 931AN: 1458602Hom.: 0 Cov.: 33 AF XY: 0.000601 AC XY: 436AN XY: 725676
GnomAD4 genome AF: 0.000440 AC: 67AN: 152224Hom.: 0 Cov.: 32 AF XY: 0.000444 AC XY: 33AN XY: 74376
ClinVar
Submissions by phenotype
Luscan-Lumish syndrome Uncertain:1Benign:1
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not provided Benign:2
SETD2: BP5, BS1 -
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not specified Benign:1
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SETD2-related disorder Benign:1
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
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at