2-71520250-CT-C
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_001130987.2(DYSF):c.1033+43delT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0458 in 1,612,022 control chromosomes in the GnomAD database, including 1,994 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001130987.2 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DYSF | ENST00000410020.8 | c.1033+43delT | intron_variant | Intron 11 of 55 | 1 | NM_001130987.2 | ENSP00000386881.3 | |||
DYSF | ENST00000258104.8 | c.937+43delT | intron_variant | Intron 10 of 54 | 1 | NM_003494.4 | ENSP00000258104.3 |
Frequencies
GnomAD3 genomes AF: 0.0362 AC: 5516AN: 152172Hom.: 124 Cov.: 32
GnomAD3 exomes AF: 0.0349 AC: 8774AN: 251478Hom.: 188 AF XY: 0.0359 AC XY: 4882AN XY: 135914
GnomAD4 exome AF: 0.0468 AC: 68387AN: 1459734Hom.: 1870 Cov.: 32 AF XY: 0.0464 AC XY: 33679AN XY: 726390
GnomAD4 genome AF: 0.0363 AC: 5522AN: 152288Hom.: 124 Cov.: 32 AF XY: 0.0342 AC XY: 2544AN XY: 74448
ClinVar
Submissions by phenotype
not specified Benign:1
- -
not provided Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at