22-47875964-A-T

Variant names:

• chr22-47875964-A-T
• rs728591
• ENST00000650660.1:n.820-52780A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000650660.1(EPIC1):​n.820-52780A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 151,778 control chromosomes in the GnomAD database, including 4,092 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 0.22 (4092 hom., cov: 33)
• Consequence: EPIC1 ENST00000650660.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 3 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 = 0.536 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650660.1. 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	ENST00000650660.1		n.820-52780A>T		intron	N/A
	EPIC1	ENST00000650683.1		n.1024-52780A>T		intron	N/A
	EPIC1	ENST00000651003.1		n.771-71602A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33281 AN: 151660 Hom.: 4088 Cov.: 33

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.219 AC: 33297 AN: 151778 Hom.: 4092 Cov.: 33 AF XY: 0.221 AC XY: 16414 AN XY: 74130

African (AFR) AF: 0.175 AC: 7263 AN: 41392

American (AMR) AF: 0.185 AC: 2820 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 693 AN: 3464

East Asian (EAS) AF: 0.553 AC: 2851 AN: 5156

South Asian (SAS) AF: 0.301 AC: 1451 AN: 4822

European-Finnish (FIN) AF: 0.217 AC: 2282 AN: 10494

Middle Eastern (MID) AF: 0.250 AC: 73 AN: 292

European-Non Finnish (NFE) AF: 0.224 AC: 15177 AN: 67880

Other (OTH) AF: 0.217 AC: 457 AN: 2110

Alfa AF: 0.224 Hom.: 528

Bravo AF: 0.214

Asia WGS AF: 0.366 AC: 1265 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.27
DANN	Benign	0.51
PhyloP100		-1.3

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: rs728591;

hg19: chr22-48271713;