rs761917

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000449941.2. 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	ENST00000449941.2	TSL:3	n.762G>T		non_coding_transcript_exon	Exon 2 of 2
	EPIC1	ENST00000651056.1		n.1260G>T		non_coding_transcript_exon	Exon 7 of 7
	EPIC1	ENST00000651294.1		n.1353G>T		non_coding_transcript_exon	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

African (AFR) AF: 0.445 AC: 18432 AN: 41386

American (AMR) AF: 0.605 AC: 9228 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.530 AC: 1838 AN: 3470

East Asian (EAS) AF: 0.744 AC: 3813 AN: 5128

South Asian (SAS) AF: 0.525 AC: 2527 AN: 4814

European-Finnish (FIN) AF: 0.547 AC: 5758 AN: 10534

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.543 AC: 36851 AN: 67928

Other (OTH) AF: 0.536 AC: 1127 AN: 2104

Alfa AF: 0.542 Hom.: 94716

Bravo AF: 0.528

Asia WGS AF: 0.635 AC: 2207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.4
DANN	Benign	0.78
PhyloP100		0.84

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: rs761917;

hg19: chr22-48258293;