rs375521654
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001723.7(DST):c.3485C>T(p.Pro1162Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000156 in 1,613,674 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 (★). Synonymous variant affecting the same amino acid position (i.e. P1162P) has been classified as Likely benign.
Frequency
Consequence
NM_001723.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DST | NM_001723.7 | c.3485C>T | p.Pro1162Leu | missense_variant | 23/24 | ENST00000370765.11 | |
DST | NM_001374736.1 | c.4929+3981C>T | intron_variant | ENST00000680361.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DST | ENST00000370765.11 | c.3485C>T | p.Pro1162Leu | missense_variant | 23/24 | 1 | NM_001723.7 | ||
DST | ENST00000680361.1 | c.4929+3981C>T | intron_variant | NM_001374736.1 |
Frequencies
GnomAD3 genomes AF: 0.000237 AC: 36AN: 152000Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000391 AC: 98AN: 250896Hom.: 0 AF XY: 0.000398 AC XY: 54AN XY: 135598
GnomAD4 exome AF: 0.000147 AC: 215AN: 1461674Hom.: 1 Cov.: 34 AF XY: 0.000150 AC XY: 109AN XY: 727142
GnomAD4 genome AF: 0.000237 AC: 36AN: 152000Hom.: 0 Cov.: 32 AF XY: 0.000377 AC XY: 28AN XY: 74234
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 | Dec 03, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at