20-50935231-T-C
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 2P and 17B. PM2BP4_StrongBP6_Very_StrongBP7BS1
The NM_003859.3(DPM1):āc.684A>Gā(p.Pro228Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000418 in 1,578,484 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_003859.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DPM1 | NM_003859.3 | c.684A>G | p.Pro228Pro | synonymous_variant | Exon 9 of 9 | ENST00000371588.10 | NP_003850.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000691 AC: 9AN: 130280Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000403 AC: 10AN: 247978Hom.: 0 AF XY: 0.0000447 AC XY: 6AN XY: 134174
GnomAD4 exome AF: 0.0000394 AC: 57AN: 1448132Hom.: 0 Cov.: 27 AF XY: 0.0000430 AC XY: 31AN XY: 721408
GnomAD4 genome AF: 0.0000690 AC: 9AN: 130352Hom.: 0 Cov.: 33 AF XY: 0.0000787 AC XY: 5AN XY: 63550
ClinVar
Submissions by phenotype
not specified 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. -
Congenital disorder of glycosylation type 1E Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at