rs1003871860
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_ModerateBP6_Moderate
The NM_004409.5(DMPK):c.1837G>T(p.Ala613Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000271 in 1,550,822 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_004409.5 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 |
---|---|---|---|---|---|---|---|
DMPK | NM_004409.5 | c.1837G>T | p.Ala613Ser | missense_variant | 15/15 | ENST00000291270.9 | |
DM1-AS | NR_147193.1 | n.337-949C>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DMPK | ENST00000291270.9 | c.1837G>T | p.Ala613Ser | missense_variant | 15/15 | 5 | NM_004409.5 | A2 | |
DM1-AS | ENST00000590076.2 | n.337-949C>A | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152250Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000194 AC: 3AN: 154698Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 81904
GnomAD4 exome AF: 0.0000272 AC: 38AN: 1398454Hom.: 0 Cov.: 32 AF XY: 0.0000203 AC XY: 14AN XY: 689814
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152368Hom.: 0 Cov.: 34 AF XY: 0.0000134 AC XY: 1AN XY: 74504
ClinVar
Submissions by phenotype
Steinert myotonic dystrophy syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genomic Research Center, Shahid Beheshti University of Medical Sciences | May 03, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at