chr20-50935231-T-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_003859.3(DPM1):c.684A>C(p.Pro228=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000691 in 1,448,132 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 (★). Synonymous variant affecting the same amino acid position (i.e. P228P) has been classified as Likely benign.
Frequency
Consequence
NM_003859.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DPM1 | NM_003859.3 | c.684A>C | p.Pro228= | synonymous_variant | 9/9 | ENST00000371588.10 | |
ADNP-AS1 | NR_110008.1 | n.149+3782T>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DPM1 | ENST00000371588.10 | c.684A>C | p.Pro228= | synonymous_variant | 9/9 | 1 | NM_003859.3 | P1 | |
ADNP-AS1 | ENST00000558899.2 | n.149+3782T>G | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000403 AC: 1AN: 247978Hom.: 0 AF XY: 0.00000745 AC XY: 1AN XY: 134174
GnomAD4 exome AF: 6.91e-7 AC: 1AN: 1448132Hom.: 0 Cov.: 27 AF XY: 0.00000139 AC XY: 1AN XY: 721408
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Congenital disorder of glycosylation type 1E Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 02, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at