rs761917

Variant names:

• chr22-47862544-G-T
• rs761917
• ENST00000449941.2:n.762G>T

Variant summary

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

The ENST00000449941.2(EPIC1):​n.762G>T variant causes a non coding transcript exon 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 ENST00000449941.2 non_coding_transcript_exon
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EPIC1	ENST00000449941.2	n.762G>T		non_coding_transcript_exon_variant	Exon 2 of 2	3
EPIC1	ENST00000651056.1	n.1260G>T		non_coding_transcript_exon_variant	Exon 7 of 7
EPIC1	ENST00000651294.1	n.1353G>T		non_coding_transcript_exon_variant	Exon 8 of 8

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;