rs372435739
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001374736.1(DST):c.2491-8G>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,754 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/2 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001374736.1 splice_region, splice_polypyrimidine_tract, intron
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_001374736.1 | c.2491-8G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000680361.1 | |||
DST | NM_001723.7 | c.880-8G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000370765.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DST | ENST00000370765.11 | c.880-8G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001723.7 | ||||
DST | ENST00000680361.1 | c.2491-8G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | NM_001374736.1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 250148Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135646
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461754Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 727166
GnomAD4 genome ? Cov.: 32
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 | Nov 16, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at