Genetic Variant EPIC1:n.1126-3909T>C (chr22-47851002-T-C) – 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.1126-3909T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0428 in 152,142 control chromosomes in the GnomAD database, including 310 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 0.043 ( 310 hom., cov: 32)

Consequence

EPIC1
ENST00000423737.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.00

Publications

0 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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EPIC1	NR_122046.1 link	n.1126-3909T>C		intron_variant	Intron 8 of 8

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
EPIC1	ENST00000423737.5 link	n.1126-3909T>C	intron_variant	Intron 8 of 8	2
EPIC1	ENST00000650660.1 link	n.820-77742T>C	intron_variant	Intron 6 of 6
EPIC1	ENST00000650683.1 link	n.1024-77742T>C	intron_variant	Intron 7 of 7

Frequencies

GnomAD3 genomes

AF:

0.0426

AC:

6471

AN:

152024

Hom.:

303

Cov.:

show subpopulations

Gnomad AFR

AF:

0.110

Gnomad AMI

AF:

0.0526

Gnomad AMR

AF:

0.0217

Gnomad ASJ

AF:

0.0170

Gnomad EAS

AF:

0.0915

Gnomad SAS

AF:

0.0268

Gnomad FIN

AF:

0.0192

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00907

Gnomad OTH

AF:

0.0268

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

GnomAD4 genome

AF:

0.0428

AC:

6512

AN:

152142

Hom.:

310

Cov.:

AF XY:

0.0422

AC XY:

3137

AN XY:

74360

show subpopulations

African (AFR)

AF:

0.111

AC:

4588

AN:

41488

American (AMR)

AF:

0.0217

AC:

332

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.0170

AC:

AN:

3472

East Asian (EAS)

AF:

0.0916

AC:

473

AN:

5166

South Asian (SAS)

AF:

0.0274

AC:

132

AN:

4818

European-Finnish (FIN)

AF:

0.0192

AC:

203

AN:

10582

Middle Eastern (MID)

AF:

0.00680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00907

AC:

617

AN:

68006

Other (OTH)

AF:

0.0274

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

294

588

883

1177

1471

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0459

Hom.:

146

Bravo

AF:

0.0480

Asia WGS

AF:

0.0410

AC:

142

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.012

(source)

DANN

Benign

0.55

PhyloP100

-4.0

Splicing

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

Publications

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chr22-47851002-T-C

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