rs371953347
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBS1BS2
The NM_014159.7(SETD2):c.2072C>T(p.Thr691Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000279 in 1,614,118 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_014159.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SETD2 | NM_014159.7 | c.2072C>T | p.Thr691Ile | missense_variant | 3/21 | ENST00000409792.4 | NP_054878.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SETD2 | ENST00000409792.4 | c.2072C>T | p.Thr691Ile | missense_variant | 3/21 | 5 | NM_014159.7 | ENSP00000386759.3 |
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152214Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251066Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135706
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1461786Hom.: 0 Cov.: 34 AF XY: 0.0000165 AC XY: 12AN XY: 727192
GnomAD4 genome AF: 0.000151 AC: 23AN: 152332Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74494
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 14, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Luscan-Lumish syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 11, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at