chr6-56617094-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001723.7(DST):c.6373G>A(p.Val2125Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000375 in 1,613,868 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001723.7 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
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.6373G>A | p.Val2125Ile | missense_variant | 24/24 | ENST00000370765.11 | |
DST | NM_001374736.1 | c.4930-2610G>A | intron_variant | ENST00000680361.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DST | ENST00000370765.11 | c.6373G>A | p.Val2125Ile | missense_variant | 24/24 | 1 | NM_001723.7 | ||
DST | ENST00000680361.1 | c.4930-2610G>A | intron_variant | NM_001374736.1 |
Frequencies
GnomAD3 genomes AF: 0.00197 AC: 300AN: 152176Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000570 AC: 143AN: 250874Hom.: 0 AF XY: 0.000376 AC XY: 51AN XY: 135584
GnomAD4 exome AF: 0.000207 AC: 303AN: 1461574Hom.: 0 Cov.: 34 AF XY: 0.000171 AC XY: 124AN XY: 727050
GnomAD4 genome AF: 0.00198 AC: 302AN: 152294Hom.: 1 Cov.: 32 AF XY: 0.00192 AC XY: 143AN XY: 74464
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 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at