rs141629958
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_004409.5(DMPK):c.882+8C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00491 in 1,613,900 control chromosomes in the GnomAD database, including 41 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_004409.5 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DMPK | NM_004409.5 | c.882+8C>T | splice_region_variant, intron_variant | ENST00000291270.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DMPK | ENST00000291270.9 | c.882+8C>T | splice_region_variant, intron_variant | 5 | NM_004409.5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00382 AC: 582AN: 152244Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00564 AC: 1416AN: 251006Hom.: 8 AF XY: 0.00645 AC XY: 876AN XY: 135750
GnomAD4 exome AF: 0.00503 AC: 7346AN: 1461538Hom.: 40 Cov.: 31 AF XY: 0.00546 AC XY: 3973AN XY: 727066
GnomAD4 genome ? AF: 0.00383 AC: 584AN: 152362Hom.: 1 Cov.: 32 AF XY: 0.00384 AC XY: 286AN XY: 74504
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Sep 25, 2017 | - - |
not specified Benign:1
Benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at