6-56639763-G-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 3P and 12B. PM2PP2BP4_StrongBP6_Very_Strong
The NM_001374736.1(DST):c.2630C>T(p.Thr877Ile) variant causes a missense change. The variant allele was found at a frequency of 0.000175 in 1,613,452 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T877A) has been classified as Uncertain significance.
Frequency
Consequence
NM_001374736.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DST | NM_001374736.1 | c.2630C>T | p.Thr877Ile | missense_variant | 20/104 | ENST00000680361.1 | |
DST | NM_001723.7 | c.1019C>T | p.Thr340Ile | missense_variant | 6/24 | ENST00000370765.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DST | ENST00000680361.1 | c.2630C>T | p.Thr877Ile | missense_variant | 20/104 | NM_001374736.1 | |||
DST | ENST00000370765.11 | c.1019C>T | p.Thr340Ile | missense_variant | 6/24 | 1 | NM_001723.7 |
Frequencies
GnomAD3 genomes AF: 0.000349 AC: 53AN: 152012Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000479 AC: 120AN: 250592Hom.: 0 AF XY: 0.000413 AC XY: 56AN XY: 135666
GnomAD4 exome AF: 0.000157 AC: 229AN: 1461326Hom.: 1 Cov.: 33 AF XY: 0.000154 AC XY: 112AN XY: 726998
GnomAD4 genome AF: 0.000348 AC: 53AN: 152126Hom.: 0 Cov.: 32 AF XY: 0.000390 AC XY: 29AN XY: 74362
ClinVar
Submissions by phenotype
Hereditary sensory and autonomic neuropathy type 6;C3809470:Epidermolysis bullosa simplex 3, localized or generalized intermediate, with BP230 deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 05, 2024 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 06, 2019 | 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