rs35014998
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001374736.1(DST):c.4590T>G(p.Asn1530Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00439 in 1,613,758 control chromosomes in the GnomAD database, including 224 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001374736.1 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DST | ENST00000680361.1 | c.4590T>G | p.Asn1530Lys | missense_variant | Exon 33 of 104 | NM_001374736.1 | ENSP00000505098.1 | |||
DST | ENST00000370765.11 | c.2979T>G | p.Asn993Lys | missense_variant | Exon 19 of 24 | 1 | NM_001723.7 | ENSP00000359801.6 |
Frequencies
GnomAD3 genomes AF: 0.0220 AC: 3351AN: 151976Hom.: 106 Cov.: 32
GnomAD3 exomes AF: 0.00616 AC: 1548AN: 251370Hom.: 44 AF XY: 0.00458 AC XY: 622AN XY: 135860
GnomAD4 exome AF: 0.00254 AC: 3716AN: 1461664Hom.: 115 Cov.: 31 AF XY: 0.00225 AC XY: 1637AN XY: 727146
GnomAD4 genome AF: 0.0222 AC: 3373AN: 152094Hom.: 109 Cov.: 32 AF XY: 0.0221 AC XY: 1644AN XY: 74354
ClinVar
Submissions by phenotype
not provided Benign:2
- -
- -
Hereditary sensory and autonomic neuropathy type 6;C3809470:Epidermolysis bullosa simplex 3, localized or generalized intermediate, with BP230 deficiency Benign:1
- -
DST-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Hereditary sensory and autonomic neuropathy type 6 Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at