dbSNP rs11912108: EPIC1:n.370-16066T>G (chr22-47997675-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000651033.1(EPIC1):n.370-16066T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0666 in 152,098 control chromosomes in the GnomAD database, including 947 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 0.067 ( 947 hom., cov: 32)

Consequence

EPIC1
ENST00000651033.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.268

Variant links:

Genes affected

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

EPIC1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.209 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	ENST00000651033.1 link	n.370-16066T>G	intron_variant	Intron 4 of 6
EPIC1	ENST00000651403.1 link	n.747-16066T>G	intron_variant	Intron 5 of 8
EPIC1	ENST00000652228.1 link	n.880-16066T>G	intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes

AF:

0.0664

AC:

10098

AN:

151980

Hom.:

942

Cov.:

show subpopulations

Gnomad AFR

AF:

0.213

Gnomad AMI

AF:

0.0197

Gnomad AMR

AF:

0.0255

Gnomad ASJ

AF:

0.00259

Gnomad EAS

AF:

0.0699

Gnomad SAS

AF:

0.00541

Gnomad FIN

AF:

0.00141

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.00544

Gnomad OTH

AF:

0.0535

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

GnomAD4 genome

AF:

0.0666

AC:

10126

AN:

152098

Hom.:

947

Cov.:

AF XY:

0.0650

AC XY:

4833

AN XY:

74350

show subpopulations

Gnomad4 AFR

AF:

0.213

Gnomad4 AMR

AF:

0.0254

Gnomad4 ASJ

AF:

0.00259

Gnomad4 EAS

AF:

0.0698

Gnomad4 SAS

AF:

0.00520

Gnomad4 FIN

AF:

0.00141

Gnomad4 NFE

AF:

0.00544

Gnomad4 OTH

AF:

0.0530

Alfa

AF:

0.0410

Hom.:

Bravo

AF:

0.0760

Asia WGS

AF:

0.0380

AC:

131

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

5.1

DANN

Benign

0.84

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over