22-47862544-G-T

Position:

• chr22-47862544-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000651403.1(EPIC1):​n.747-151197G>T 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 0.528 in 151,834 control chromosomes in the GnomAD database, including 21,633 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 0.53 (21633 hom., cov: 31)
• Consequence: EPIC1 ENST00000651403.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.836

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.724 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.747-151197G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80079 AN: 151714 Hom.: 21618 Cov.: 31

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.604

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.528 AC: 80137 AN: 151834 Hom.: 21633 Cov.: 31 AF XY: 0.529 AC XY: 39262 AN XY: 74220

Gnomad4 AFR AF: 0.445

Gnomad4 AMR AF: 0.605

Gnomad4 ASJ AF: 0.530

Gnomad4 EAS AF: 0.744

Gnomad4 SAS AF: 0.525

Gnomad4 FIN AF: 0.547

Gnomad4 NFE AF: 0.543

Gnomad4 OTH AF: 0.536

Alfa AF: 0.543 Hom.: 45696

Bravo AF: 0.528

Asia WGS AF: 0.635 AC: 2207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.4
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs761917; hg19: chr22-48258293;