rs202179816
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_001080517.3(SETD5):c.3944C>T(p.Thr1315Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000688 in 1,613,846 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). Synonymous variant affecting the same amino acid position (i.e. T1315T) has been classified as Likely benign.
Frequency
Consequence
NM_001080517.3 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 |
---|---|---|---|---|---|---|---|
SETD5 | NM_001080517.3 | c.3944C>T | p.Thr1315Met | missense_variant | 23/23 | ENST00000402198.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SETD5 | ENST00000402198.7 | c.3944C>T | p.Thr1315Met | missense_variant | 23/23 | 5 | NM_001080517.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000355 AC: 54AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000924 AC: 23AN: 248982Hom.: 0 AF XY: 0.0000888 AC XY: 12AN XY: 135096
GnomAD4 exome AF: 0.0000390 AC: 57AN: 1461690Hom.: 0 Cov.: 31 AF XY: 0.0000344 AC XY: 25AN XY: 727128
GnomAD4 genome ? AF: 0.000355 AC: 54AN: 152156Hom.: 0 Cov.: 32 AF XY: 0.000363 AC XY: 27AN XY: 74320
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 06, 2023 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | May 26, 2021 | - - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Mar 31, 2017 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 17, 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at