rs410509
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1
The NM_014674.3(EDEM1):c.615C>A(p.Ala205=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.965 in 1,613,392 control chromosomes in the GnomAD database, including 752,632 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.95 ( 68148 hom., cov: 33)
Exomes 𝑓: 0.97 ( 684484 hom. )
Consequence
EDEM1
NM_014674.3 synonymous
NM_014674.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.95
Genes affected
EDEM1 (HGNC:18967): (ER degradation enhancing alpha-mannosidase like protein 1) Enables mannosyl-oligosaccharide 1,2-alpha-mannosidase activity and misfolded protein binding activity. Involved in mannose trimming involved in glycoprotein ERAD pathway; positive regulation of retrograde protein transport, ER to cytosol; and protein targeting to ER. Located in aggresome and endoplasmic reticulum quality control compartment. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.34).
BP7
?
Synonymous conserved (PhyloP=-1.95 with no splicing effect.
BA1
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GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.969 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EDEM1 | NM_014674.3 | c.615C>A | p.Ala205= | synonymous_variant | 3/12 | ENST00000256497.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EDEM1 | ENST00000256497.9 | c.615C>A | p.Ala205= | synonymous_variant | 3/12 | 1 | NM_014674.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.945 AC: 143839AN: 152172Hom.: 68110 Cov.: 33
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GnomAD3 exomes AF: 0.959 AC: 240508AN: 250906Hom.: 115472 AF XY: 0.958 AC XY: 129855AN XY: 135618
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GnomAD4 exome AF: 0.968 AC: 1413686AN: 1461102Hom.: 684484 Cov.: 40 AF XY: 0.966 AC XY: 701952AN XY: 726874
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GnomAD4 genome ? AF: 0.945 AC: 143935AN: 152290Hom.: 68148 Cov.: 33 AF XY: 0.944 AC XY: 70338AN XY: 74478
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at