rs1028528

Positions:

• 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 ENST00000651403.1(EPIC1):​n.747-47200A>G variant causes a intron, non coding transcript 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 ENST00000651403.1 intron, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EPIC1	ENST00000651403.1	n.747-47200A>G		intron_variant, non_coding_transcript_variant

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;