Genetic Variant EPIC1:n.982+9763A>G (chr22-47714510-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000423737.5(EPIC1):n.982+9763A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 151,982 control chromosomes in the GnomAD database, including 10,115 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 0.34 ( 10115 hom., cov: 33)

Consequence

EPIC1
ENST00000423737.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.46

Publications

1 publications found

Variant links:

Genes affected

EPIC1 (HGNC:27672): (epigenetically induced MYC interacting lncRNA 1)

EPIC1 links:

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=-0.98).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EPIC1	NR_122046.1 link	n.982+9763A>G		intron_variant	Intron 7 of 8

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
EPIC1	ENST00000423737.5 link	n.982+9763A>G	intron_variant	Intron 7 of 8	2
EPIC1	ENST00000650660.1 link	n.819+27304A>G	intron_variant	Intron 6 of 6
EPIC1	ENST00000650683.1 link	n.1023+9763A>G	intron_variant	Intron 7 of 7

Frequencies

GnomAD3 genomes

AF:

0.341

AC:

51811

AN:

151864

Hom.:

10099

Cov.:

show subpopulations

Gnomad AFR

AF:

0.197

Gnomad AMI

AF:

0.336

Gnomad AMR

AF:

0.496

Gnomad ASJ

AF:

0.312

Gnomad EAS

AF:

0.673

Gnomad SAS

AF:

0.612

Gnomad FIN

AF:

0.359

Gnomad MID

AF:

0.342

Gnomad NFE

AF:

0.348

Gnomad OTH

AF:

0.358

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.341

AC:

51848

AN:

151982

Hom.:

10115

Cov.:

AF XY:

0.352

AC XY:

26126

AN XY:

74262

show subpopulations

African (AFR)

AF:

0.197

AC:

8163

AN:

41490

American (AMR)

AF:

0.497

AC:

7602

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.312

AC:

1083

AN:

3468

East Asian (EAS)

AF:

0.673

AC:

3463

AN:

5144

South Asian (SAS)

AF:

0.612

AC:

2945

AN:

4816

European-Finnish (FIN)

AF:

0.359

AC:

3785

AN:

10556

Middle Eastern (MID)

AF:

0.344

AC:

101

AN:

294

European-Non Finnish (NFE)

AF:

0.348

AC:

23639

AN:

67908

Other (OTH)

AF:

0.361

AC:

761

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1638

3277

4915

6554

8192

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.365

Hom.:

6017

Bravo

AF:

0.344

Asia WGS

AF:

0.601

AC:

2091

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

1.8

(source)

DANN

Benign

0.28

PhyloP100

-1.5

Splicing

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

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.

chr22-47714510-A-G

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over