rs11912108

Variant names:

• chr22-47997675-T-G
• rs11912108
• ENST00000651033.2:n.370-16066T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000651033.2(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 ENST00000651033.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.268
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EPIC1	ENST00000651033.2	n.370-16066T>G		intron_variant	Intron 4 of 9
EPIC1	ENST00000651403.1	n.747-16066T>G		intron_variant	Intron 5 of 8
EPIC1	ENST00000652228.1	n.880-16066T>G		intron_variant	Intron 6 of 6
EPIC1	ENST00000809073.1	n.1045-16066T>G		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.0664 AC: 10098 AN: 151980 Hom.: 942 Cov.: 32

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.: 32 AF XY: 0.0650 AC XY: 4833 AN XY: 74350

African (AFR) AF: 0.213 AC: 8827 AN: 41448

American (AMR) AF: 0.0254 AC: 388 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.00259 AC: 9 AN: 3470

East Asian (EAS) AF: 0.0698 AC: 359 AN: 5140

South Asian (SAS) AF: 0.00520 AC: 25 AN: 4806

European-Finnish (FIN) AF: 0.00141 AC: 15 AN: 10610

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.00544 AC: 370 AN: 68008

Other (OTH) AF: 0.0530 AC: 112 AN: 2114

Alfa AF: 0.0392 Hom.: 142

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
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs11912108; hg19: chr22-48393424;