rs738733

Variant names:

• chr22-47899668-A-C
• rs738733
• ENST00000650660.1:n.820-29076A>C

Your query was ambiguous. Multiple possible variants found:

• chr22-47899668-A-C
• chr22-47899668-A-T

Variant summary

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

The ENST00000650660.1(EPIC1):​n.820-29076A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.453 in 152,036 control chromosomes in the GnomAD database, including 15,828 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 0.45 (15828 hom., cov: 33)
• Consequence: EPIC1 ENST00000650660.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.73
• 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=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.494 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EPIC1	ENST00000650660.1		n.820-29076A>C		intron	N/A
	EPIC1	ENST00000650683.1		n.1024-29076A>C		intron	N/A
	EPIC1	ENST00000651003.1		n.771-47898A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.453 AC: 68787 AN: 151918 Hom.: 15827 Cov.: 33

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.453 AC: 68824 AN: 152036 Hom.: 15828 Cov.: 33 AF XY: 0.449 AC XY: 33354 AN XY: 74316

African (AFR) AF: 0.365 AC: 15142 AN: 41456

American (AMR) AF: 0.483 AC: 7370 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.464 AC: 1609 AN: 3470

East Asian (EAS) AF: 0.500 AC: 2587 AN: 5172

South Asian (SAS) AF: 0.398 AC: 1914 AN: 4812

European-Finnish (FIN) AF: 0.445 AC: 4696 AN: 10564

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.499 AC: 33892 AN: 67974

Other (OTH) AF: 0.475 AC: 1006 AN: 2116

Alfa AF: 0.489 Hom.: 78515

Bravo AF: 0.457

Asia WGS AF: 0.430 AC: 1494 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	12
DANN	Benign	0.73
PhyloP100		2.7

Splicing

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

Other links and lift over

dbSNP: rs738733; hg19: chr22-48295417;