Genetic Variant EPIC1:n.771-17791A>G (chr22-47929775-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 ENST00000651003.1(EPIC1):n.771-17791A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 152,212 control chromosomes in the GnomAD database, including 1,270 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 0.13 ( 1270 hom., cov: 33)

Consequence

EPIC1
ENST00000651003.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.518

Publications

2 publications found

Variant links:

Genes affected

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

EPIC1 links:

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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 (AMR) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
EPIC1	ENST00000651003.1 link	n.771-17791A>G	intron_variant	Intron 6 of 6
EPIC1	ENST00000651033.2 link	n.370-83966A>G	intron_variant	Intron 4 of 9
EPIC1	ENST00000651124.1 link	n.907-17791A>G	intron_variant	Intron 7 of 7

Frequencies

GnomAD3 genomes

AF:

0.125

AC:

19074

AN:

152094

Hom.:

1271

Cov.:

show subpopulations

Gnomad AFR

AF:

0.147

Gnomad AMI

AF:

0.0855

Gnomad AMR

AF:

0.184

Gnomad ASJ

AF:

0.162

Gnomad EAS

AF:

0.164

Gnomad SAS

AF:

0.166

Gnomad FIN

AF:

0.112

Gnomad MID

AF:

0.136

Gnomad NFE

AF:

0.0935

Gnomad OTH

AF:

0.132

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

GnomAD4 genome

AF:

0.125

AC:

19082

AN:

152212

Hom.:

1270

Cov.:

AF XY:

0.128

AC XY:

9549

AN XY:

74432

show subpopulations

African (AFR)

AF:

0.147

AC:

6114

AN:

41520

American (AMR)

AF:

0.184

AC:

2821

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.162

AC:

563

AN:

3472

East Asian (EAS)

AF:

0.163

AC:

844

AN:

5174

South Asian (SAS)

AF:

0.166

AC:

800

AN:

4832

European-Finnish (FIN)

AF:

0.112

AC:

1187

AN:

10602

Middle Eastern (MID)

AF:

0.133

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0934

AC:

6354

AN:

67994

Other (OTH)

AF:

0.133

AC:

282

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

841

1682

2522

3363

4204

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.107

Hom.:

1614

Bravo

AF:

0.133

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.20

(source)

DANN

Benign

0.40

PhyloP100

-0.52

Splicing

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

Publications

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chr22-47929775-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