rs187767340
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 1P and 14B. PP2BP4_StrongBP6_ModerateBS1BS2
The NM_014159.7(SETD2):c.335C>T(p.Ser112Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000393 in 1,551,744 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. S112S) has been classified as Likely benign.
Frequency
Consequence
NM_014159.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SETD2 | NM_014159.7 | c.335C>T | p.Ser112Leu | missense_variant | 3/21 | ENST00000409792.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SETD2 | ENST00000409792.4 | c.335C>T | p.Ser112Leu | missense_variant | 3/21 | 5 | NM_014159.7 | P3 |
Frequencies
GnomAD3 genomes AF: 0.000191 AC: 29AN: 152196Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000383 AC: 6AN: 156840Hom.: 0 AF XY: 0.0000241 AC XY: 2AN XY: 83102
GnomAD4 exome AF: 0.0000222 AC: 31AN: 1399430Hom.: 0 Cov.: 33 AF XY: 0.0000188 AC XY: 13AN XY: 690224
GnomAD4 genome AF: 0.000197 AC: 30AN: 152314Hom.: 0 Cov.: 32 AF XY: 0.000228 AC XY: 17AN XY: 74488
ClinVar
Submissions by phenotype
Luscan-Lumish syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 03, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at