rs150229184
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_001723.7(DST):c.4961C>T(p.Ala1654Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000304 in 1,613,892 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 9/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. A1654A) has been classified as Likely benign.
Frequency
Consequence
NM_001723.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DST | NM_001723.7 | c.4961C>T | p.Ala1654Val | missense_variant | 23/24 | ENST00000370765.11 | |
DST | NM_001374736.1 | c.4930-4589C>T | intron_variant | ENST00000680361.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DST | ENST00000370765.11 | c.4961C>T | p.Ala1654Val | missense_variant | 23/24 | 1 | NM_001723.7 | ||
DST | ENST00000680361.1 | c.4930-4589C>T | intron_variant | NM_001374736.1 |
Frequencies
GnomAD3 genomes ? AF: 0.00169 AC: 257AN: 152032Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000367 AC: 92AN: 250870Hom.: 0 AF XY: 0.000273 AC XY: 37AN XY: 135610
GnomAD4 exome AF: 0.000159 AC: 233AN: 1461742Hom.: 0 Cov.: 36 AF XY: 0.000135 AC XY: 98AN XY: 727178
GnomAD4 genome ? AF: 0.00169 AC: 257AN: 152150Hom.: 0 Cov.: 32 AF XY: 0.00177 AC XY: 132AN XY: 74388
ClinVar
Submissions by phenotype
not provided Uncertain:2Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 10, 2022 | In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Uncertain significance, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Uncertain significance, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
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 | Dec 11, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at