3-36988684-C-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_014805.4(EPM2AIP1):c.*2570G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.517 in 151,850 control chromosomes in the GnomAD database, including 21,381 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★★).
Frequency
Genomes: 𝑓 0.52 ( 21380 hom., cov: 31)
Exomes 𝑓: 0.50 ( 1 hom. )
Consequence
EPM2AIP1
NM_014805.4 3_prime_UTR
NM_014805.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.120
Publications
24 publications found
Genes affected
EPM2AIP1 (HGNC:19735): (EPM2A interacting protein 1) The EPM2A gene, which encodes laforin, is mutated in an autosomal recessive form of adolescent progressive myoclonus epilepsy. The protein encoded by this gene binds to laforin, but its function is not known. This gene is intronless. [provided by RefSeq, Oct 2008]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
Variant 3-36988684-C-A is Benign according to our data. Variant chr3-36988684-C-A is described in ClinVar as [Benign]. Clinvar id is 89594.Status of the report is reviewed_by_expert_panel, 3 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EPM2AIP1 | ENST00000322716.8 | c.*2570G>T | 3_prime_UTR_variant | Exon 1 of 1 | 6 | NM_014805.4 | ENSP00000406027.1 | |||
EPM2AIP1 | ENST00000623924.1 | c.123-1455G>T | intron_variant | Intron 2 of 2 | 5 | ENSP00000485489.1 |
Frequencies
GnomAD3 genomes AF: 0.516 AC: 78366AN: 151726Hom.: 21350 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
78366
AN:
151726
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.500 AC: 3AN: 6Hom.: 1 Cov.: 0 AF XY: 0.500 AC XY: 3AN XY: 6 show subpopulations
GnomAD4 exome
AF:
AC:
3
AN:
6
Hom.:
Cov.:
0
AF XY:
AC XY:
3
AN XY:
6
show subpopulations
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AC:
0
AN:
0
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
AC:
3
AN:
6
Other (OTH)
AC:
0
AN:
0
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.675
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.517 AC: 78453AN: 151844Hom.: 21380 Cov.: 31 AF XY: 0.507 AC XY: 37616AN XY: 74186 show subpopulations
GnomAD4 genome
AF:
AC:
78453
AN:
151844
Hom.:
Cov.:
31
AF XY:
AC XY:
37616
AN XY:
74186
show subpopulations
African (AFR)
AF:
AC:
25531
AN:
41368
American (AMR)
AF:
AC:
7412
AN:
15270
Ashkenazi Jewish (ASJ)
AF:
AC:
1633
AN:
3468
East Asian (EAS)
AF:
AC:
504
AN:
5166
South Asian (SAS)
AF:
AC:
1291
AN:
4822
European-Finnish (FIN)
AF:
AC:
4630
AN:
10516
Middle Eastern (MID)
AF:
AC:
131
AN:
290
European-Non Finnish (NFE)
AF:
AC:
35745
AN:
67928
Other (OTH)
AF:
AC:
1049
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1800
3601
5401
7202
9002
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
828
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: reviewed by expert panel
LINK: link
Submissions by phenotype
Lynch syndrome Benign:1
Sep 05, 2013
International Society for Gastrointestinal Hereditary Tumours (InSiGHT)
Significance:Benign
Review Status:reviewed by expert panel
Collection Method:research
MAF >1% -
not provided Benign:1
-
Breakthrough Genomics, Breakthrough Genomics
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:not provided
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.