rs2834070

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000454622.2(ENSG00000227757):​n.201+55760C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 152,182 control chromosomes in the GnomAD database, including 5,255 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 0.24 ( 5255 hom., cov: 33)

Consequence

ENSG00000227757
ENST00000454622.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.431

Publications

11 publications found
Variant links:
Genes affected
EPCIP-AS1 (HGNC:1290): (EPCIP antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000227757ENST00000454622.2 linkn.201+55760C>A intron_variant Intron 1 of 1 2
EPCIP-AS1ENST00000700822.1 linkn.487-4240G>T intron_variant Intron 3 of 3
ENSG00000227757ENST00000777421.1 linkn.92-33481C>A intron_variant Intron 1 of 1
ENSG00000227757ENST00000777423.1 linkn.114+11044C>A intron_variant Intron 1 of 1

Frequencies

GnomAD3 genomes
AF:
0.244
AC:
37150
AN:
152064
Hom.:
5256
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.124
Gnomad AMI
AF:
0.124
Gnomad AMR
AF:
0.210
Gnomad ASJ
AF:
0.316
Gnomad EAS
AF:
0.0568
Gnomad SAS
AF:
0.272
Gnomad FIN
AF:
0.294
Gnomad MID
AF:
0.275
Gnomad NFE
AF:
0.327
Gnomad OTH
AF:
0.267
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.244
AC:
37155
AN:
152182
Hom.:
5255
Cov.:
33
AF XY:
0.242
AC XY:
17973
AN XY:
74392
show subpopulations
African (AFR)
AF:
0.123
AC:
5124
AN:
41522
American (AMR)
AF:
0.209
AC:
3201
AN:
15296
Ashkenazi Jewish (ASJ)
AF:
0.316
AC:
1095
AN:
3470
East Asian (EAS)
AF:
0.0569
AC:
295
AN:
5184
South Asian (SAS)
AF:
0.273
AC:
1314
AN:
4822
European-Finnish (FIN)
AF:
0.294
AC:
3119
AN:
10594
Middle Eastern (MID)
AF:
0.286
AC:
84
AN:
294
European-Non Finnish (NFE)
AF:
0.327
AC:
22251
AN:
67976
Other (OTH)
AF:
0.265
AC:
559
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.499
Heterozygous variant carriers
0
1411
2822
4233
5644
7055
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
398
796
1194
1592
1990
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.302
Hom.:
13943
Bravo
AF:
0.233
Asia WGS
AF:
0.134
AC:
466
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
1.4
DANN
Benign
0.44
PhyloP100
0.43

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs2834070; hg19: chr21-34387452; API