chr2-47224689-G-C

Variant names:

• chr2-47224689-G-C
• rs12612040
• ENST00000419035.1:n.67-3366C>G

Variant summary

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

The ENST00000419035.1(EPCAM-DT):​n.67-3366C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 152,022 control chromosomes in the GnomAD database, including 18,394 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 0.43 (18394 hom., cov: 31)
• Consequence: EPCAM-DT ENST00000419035.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.205
• Publications: 2 publications found

Genes affected

EPCAM-DT (HGNC:52639): (EPCAM divergent transcript)

ENSG00000226087 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000419035.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EPCAM-DT	NR_110207.1		n.175-3366C>G		intron	N/A
	EPCAM-DT	NR_110208.1		n.404-25146C>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EPCAM-DT	ENST00000419035.1	TSL:2	n.67-3366C>G		intron	N/A
	EPCAM-DT	ENST00000441997.5	TSL:4	n.404-25146C>G		intron	N/A
	EPCAM-DT	ENST00000448713.5	TSL:4	n.165-31872C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64883 AN: 151904 Hom.: 18343 Cov.: 31

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.428 AC: 64991 AN: 152022 Hom.: 18394 Cov.: 31 AF XY: 0.419 AC XY: 31109 AN XY: 74278

African (AFR) AF: 0.818 AC: 33916 AN: 41468

American (AMR) AF: 0.290 AC: 4431 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1076 AN: 3466

East Asian (EAS) AF: 0.288 AC: 1488 AN: 5170

South Asian (SAS) AF: 0.339 AC: 1634 AN: 4816

European-Finnish (FIN) AF: 0.226 AC: 2392 AN: 10572

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 19005 AN: 67946

Other (OTH) AF: 0.371 AC: 783 AN: 2108

Alfa AF: 0.173 Hom.: 283

Bravo AF: 0.449

Asia WGS AF: 0.345 AC: 1202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.72
DANN	Benign	0.48
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs12612040; hg19: chr2-47451828;