rs9627183

Variant names:

• chr22-47888765-G-A
• rs9627183
• ENST00000650660.1:n.820-39979G>A

Variant summary

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

The ENST00000650660.1(EPIC1):​n.820-39979G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0519 in 152,202 control chromosomes in the GnomAD database, including 314 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 0.052 (314 hom., cov: 33)
• Consequence: EPIC1 ENST00000650660.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.533
• Publications: 7 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650660.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EPIC1	ENST00000650660.1		n.820-39979G>A		intron	N/A
	EPIC1	ENST00000650683.1		n.1024-39979G>A		intron	N/A
	EPIC1	ENST00000651003.1		n.771-58801G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0519 AC: 7886 AN: 152084 Hom.: 314 Cov.: 33

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.0187

Gnomad AMR AF: 0.0290

Gnomad ASJ AF: 0.0357

Gnomad EAS AF: 0.0663

Gnomad SAS AF: 0.0562

Gnomad FIN AF: 0.0258

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0289

Gnomad OTH AF: 0.0483

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

GnomAD4 genome AF: 0.0519 AC: 7903 AN: 152202 Hom.: 314 Cov.: 33 AF XY: 0.0509 AC XY: 3791 AN XY: 74418

African (AFR) AF: 0.105 AC: 4353 AN: 41506

American (AMR) AF: 0.0289 AC: 443 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0357 AC: 124 AN: 3472

East Asian (EAS) AF: 0.0665 AC: 344 AN: 5176

South Asian (SAS) AF: 0.0565 AC: 272 AN: 4814

European-Finnish (FIN) AF: 0.0258 AC: 273 AN: 10594

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0289 AC: 1965 AN: 68020

Other (OTH) AF: 0.0478 AC: 101 AN: 2112

Alfa AF: 0.0401 Hom.: 318

Bravo AF: 0.0550

Asia WGS AF: 0.0540 AC: 186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.59
DANN	Benign	0.63
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs9627183; hg19: chr22-48284514;