20-50935242-T-TAA
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_003859.3(DPM1):c.679-7_679-6insTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00337 in 1,543,996 control chromosomes in the GnomAD database, including 95 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_003859.3 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DPM1 | NM_003859.3 | c.679-7_679-6insTT | splice_region_variant, intron_variant | Intron 8 of 8 | ENST00000371588.10 | NP_003850.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0215 AC: 2676AN: 124312Hom.: 79 Cov.: 29
GnomAD3 exomes AF: 0.00355 AC: 835AN: 235258Hom.: 2 AF XY: 0.00249 AC XY: 319AN XY: 128104
GnomAD4 exome AF: 0.00177 AC: 2515AN: 1419624Hom.: 13 Cov.: 21 AF XY: 0.00151 AC XY: 1071AN XY: 708782
GnomAD4 genome AF: 0.0216 AC: 2684AN: 124372Hom.: 82 Cov.: 29 AF XY: 0.0208 AC XY: 1264AN XY: 60738
ClinVar
Submissions by phenotype
not provided Benign:2
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Congenital disorder of glycosylation Benign:1
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Congenital disorder of glycosylation type 1E Benign:1
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DPM1-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at