rs6120849
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_018217.3(EDEM2):c.259-106G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 758,902 control chromosomes in the GnomAD database, including 17,903 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 0.19 ( 3049 hom., cov: 32)
Exomes 𝑓: 0.21 ( 14854 hom. )
Consequence
EDEM2
NM_018217.3 intron
NM_018217.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.06
Genes affected
EDEM2 (HGNC:15877): (ER degradation enhancing alpha-mannosidase like protein 2) In the endoplasmic reticulum (ER), misfolded proteins are retrotranslocated to the cytosol and degraded by the proteasome in a process known as ER-associated degradation (ERAD). EDEM2 belongs to a family of proteins involved in ERAD of glycoproteins (Mast et al., 2005 [PubMed 15537790]).[supplied by OMIM, Mar 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EDEM2 | NM_018217.3 | c.259-106G>A | intron_variant | ENST00000374492.8 | NP_060687.2 | |||
EDEM2 | NM_001145025.2 | c.148-106G>A | intron_variant | NP_001138497.1 | ||||
MMP24-AS1-EDEM2 | NM_001355008.2 | c.136-106G>A | intron_variant | NP_001341937.1 | ||||
EDEM2 | NR_026728.2 | n.553-106G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EDEM2 | ENST00000374492.8 | c.259-106G>A | intron_variant | 1 | NM_018217.3 | ENSP00000363616.3 | ||||
EDEM2 | ENST00000374491.3 | c.148-106G>A | intron_variant | 1 | ENSP00000363615.2 |
Frequencies
GnomAD3 genomes AF: 0.193 AC: 29254AN: 151860Hom.: 3048 Cov.: 32
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GnomAD4 exome AF: 0.212 AC: 128644AN: 606924Hom.: 14854 AF XY: 0.215 AC XY: 68867AN XY: 320902
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GnomAD4 genome AF: 0.193 AC: 29265AN: 151978Hom.: 3049 Cov.: 32 AF XY: 0.194 AC XY: 14399AN XY: 74278
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at