rs1028528

Variant names:

• chr22-47966541-A-G
• rs1028528
• ENST00000651033.1: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. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000651033.1(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 ENST00000651033.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.48

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

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	ENST00000651033.1	n.370-47200A>G		intron_variant	Intron 4 of 6
EPIC1	ENST00000651403.1	n.747-47200A>G		intron_variant	Intron 5 of 8
EPIC1	ENST00000651445.1	n.854-7631A>G		intron_variant	Intron 6 of 6

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

Gnomad4 AFR AF: 0.723

Gnomad4 AMR AF: 0.273

Gnomad4 ASJ AF: 0.362

Gnomad4 EAS AF: 0.355

Gnomad4 SAS AF: 0.344

Gnomad4 FIN AF: 0.208

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.374

Alfa AF: 0.269 Hom.: 1639

Bravo AF: 0.409

Asia WGS AF: 0.402 AC: 1397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1028528; hg19: chr22-48362290;