rs1028528

Variant names:

• chr22-47966541-A-G
• rs1028528
• ENST00000651033.2:n.370-47200A>G

Your query was ambiguous. Multiple possible variants found:

• chr22-47966541-A-G
• chr22-47966541-A-T

Variant summary

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

The ENST00000651033.2(EPIC1):​n.370-47200A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.392 in 152,078 control chromosomes in the GnomAD database, including 14,919 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 0.39 (14919 hom., cov: 32)
• Consequence: EPIC1 ENST00000651033.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.48
• Publications: 19 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.716 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000651033.2. 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	ENST00000651033.2		n.370-47200A>G		intron	N/A
	EPIC1	ENST00000651403.1		n.747-47200A>G		intron	N/A
	EPIC1	ENST00000651445.1		n.854-7631A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.391 AC: 59432 AN: 151960 Hom.: 14867 Cov.: 32

Gnomad AFR AF: 0.723

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.338

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.392 AC: 59543 AN: 152078 Hom.: 14919 Cov.: 32 AF XY: 0.386 AC XY: 28671 AN XY: 74350

African (AFR) AF: 0.723 AC: 29984 AN: 41462

American (AMR) AF: 0.273 AC: 4178 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1255 AN: 3470

East Asian (EAS) AF: 0.355 AC: 1832 AN: 5160

South Asian (SAS) AF: 0.344 AC: 1659 AN: 4818

European-Finnish (FIN) AF: 0.208 AC: 2204 AN: 10590

Middle Eastern (MID) AF: 0.346 AC: 101 AN: 292

European-Non Finnish (NFE) AF: 0.254 AC: 17292 AN: 67976

Other (OTH) AF: 0.374 AC: 790 AN: 2110

Alfa AF: 0.384 Hom.: 9169

Bravo AF: 0.409

Asia WGS AF: 0.402 AC: 1397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.017
DANN	Benign	0.43
PhyloP100		-2.5

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1028528;

hg19: chr22-48362290;