chr2-47274012-T-G

Variant names:

• chr2-47274012-T-G
• rs6728024
• ENST00000419035.1:n.67-52689A>C

Variant summary

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

The ENST00000419035.1(EPCAM-DT):​n.67-52689A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,192 control chromosomes in the GnomAD database, including 2,229 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 0.16 (2229 hom., cov: 32)
• Consequence: EPCAM-DT ENST00000419035.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.149
• Publications: 1 publications found

Genes affected

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

ENSG00000301821 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.244 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.175-52689A>C		intron	N/A
	EPCAM-DT	NR_110208.1		n.403+58261A>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EPCAM-DT	ENST00000419035.1	TSL:2	n.67-52689A>C		intron	N/A
	EPCAM-DT	ENST00000441997.5	TSL:4	n.403+58261A>C		intron	N/A
	EPCAM-DT	ENST00000448713.5	TSL:4	n.164+49409A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24366 AN: 152074 Hom.: 2224 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.0244

Gnomad SAS AF: 0.0898

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.160 AC: 24400 AN: 152192 Hom.: 2229 Cov.: 32 AF XY: 0.158 AC XY: 11783 AN XY: 74434

African (AFR) AF: 0.248 AC: 10292 AN: 41478

American (AMR) AF: 0.105 AC: 1607 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 569 AN: 3472

East Asian (EAS) AF: 0.0243 AC: 126 AN: 5186

South Asian (SAS) AF: 0.0915 AC: 442 AN: 4830

European-Finnish (FIN) AF: 0.159 AC: 1683 AN: 10600

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9158 AN: 68016

Other (OTH) AF: 0.157 AC: 331 AN: 2108

Alfa AF: 0.104 Hom.: 203

Bravo AF: 0.163

Asia WGS AF: 0.0710 AC: 248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.0
DANN	Benign	0.79
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs6728024; hg19: chr2-47501151;