rs10169164

Variant names:

• chr2-47251652-T-A
• rs10169164
• ENST00000419035.1:n.67-30329A>T

Your query was ambiguous. Multiple possible variants found:

• chr2-47251652-T-A
• chr2-47251652-T-C
• chr2-47251652-T-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.67-30329A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.628 in 151,980 control chromosomes in the GnomAD database, including 31,042 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 0.63 (31042 hom., cov: 31)
• Consequence: EPCAM-DT ENST00000419035.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 2 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.782 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EPCAM-DT	NR_110207.1		n.175-30329A>T		intron	N/A
	EPCAM-DT	NR_110208.1		n.404-52109A>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EPCAM-DT	ENST00000419035.1	TSL:2	n.67-30329A>T		intron	N/A
	EPCAM-DT	ENST00000441997.5	TSL:4	n.404-52109A>T		intron	N/A
	EPCAM-DT	ENST00000448713.5	TSL:4	n.165-58835A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.628 AC: 95338 AN: 151862 Hom.: 30989 Cov.: 31

Gnomad AFR AF: 0.789

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.782

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.628 AC: 95459 AN: 151980 Hom.: 31042 Cov.: 31 AF XY: 0.628 AC XY: 46641 AN XY: 74282

African (AFR) AF: 0.790 AC: 32762 AN: 41492

American (AMR) AF: 0.667 AC: 10176 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.567 AC: 1963 AN: 3462

East Asian (EAS) AF: 0.782 AC: 4038 AN: 5166

South Asian (SAS) AF: 0.679 AC: 3268 AN: 4810

European-Finnish (FIN) AF: 0.494 AC: 5204 AN: 10536

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.533 AC: 36187 AN: 67948

Other (OTH) AF: 0.621 AC: 1313 AN: 2116

Alfa AF: 0.412 Hom.: 949

Bravo AF: 0.652

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.73
DANN	Benign	0.42
PhyloP100		-1.1

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: rs10169164;

hg19: chr2-47478791;