rs786205661
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PM4_SupportingPP5_Moderate
The NM_001349884.2(DRAM2):c.64_66del(p.Ala22del) variant causes a inframe deletion change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Genomes: not found (cov: 32)
Consequence
DRAM2
NM_001349884.2 inframe_deletion
NM_001349884.2 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 8.02
Genes affected
DRAM2 (HGNC:28769): (DNA damage regulated autophagy modulator 2) The protein encoded by this gene binds microtubule-associated protein 1 light chain 3 and is required for autophagy. Defects in this gene are a cause of retinal dystrophy. In addition, two microRNAs (microRNA 125b-1 and microRNA 144) can bind to the mRNA of this gene and produce the disease state. [provided by RefSeq, Mar 2017]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PM4
?
Nonframeshift variant in NON repetitive region in NM_001349884.2. Strenght limited to Supporting due to length of the change: 1aa.
PP5
?
Variant 1-111131488-AAGC-A is Pathogenic according to our data. Variant chr1-111131488-AAGC-A is described in ClinVar as [Pathogenic]. Clinvar id is 192234.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DRAM2 | NM_001349884.2 | c.64_66del | p.Ala22del | inframe_deletion | 4/10 | ENST00000484310.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DRAM2 | ENST00000484310.6 | c.64_66del | p.Ala22del | inframe_deletion | 4/10 | 1 | NM_001349884.2 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Cone-rod dystrophy 21 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | May 12, 2015 | - - |
Retinal dystrophy Pathogenic:1
Pathogenic, criteria provided, single submitter | reference population | Leeds Vision Research Group, University of Leeds | Nov 01, 2014 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
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Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at