chr2-47251652-T-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000419035.1(EPCAM-DT):​n.67-30329A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00623 in 152,050 control chromosomes in the GnomAD database, including 9 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 0.0062 (9 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=-0.96).
• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.00623 (948/152050) while in subpopulation SAS AF = 0.0322 (155/4820). AF 95% confidence interval is 0.028. There are 9 homozygotes in GnomAd4. There are 467 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 9 gene

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>C		intron	N/A
	EPCAM-DT	NR_110208.1		n.404-52109A>C		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>C		intron	N/A
	EPCAM-DT	ENST00000441997.5	TSL:4	n.404-52109A>C		intron	N/A
	EPCAM-DT	ENST00000448713.5	TSL:4	n.165-58835A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00627 AC: 952 AN: 151932 Hom.: 10 Cov.: 31

Gnomad AFR AF: 0.00157

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00518

Gnomad ASJ AF: 0.00923

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0323

Gnomad FIN AF: 0.00247

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00840

Gnomad OTH AF: 0.00860

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

GnomAD4 genome AF: 0.00623 AC: 948 AN: 152050 Hom.: 9 Cov.: 31 AF XY: 0.00628 AC XY: 467 AN XY: 74314

African (AFR) AF: 0.00157 AC: 65 AN: 41500

American (AMR) AF: 0.00511 AC: 78 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.00923 AC: 32 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5170

South Asian (SAS) AF: 0.0322 AC: 155 AN: 4820

European-Finnish (FIN) AF: 0.00247 AC: 26 AN: 10542

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.00840 AC: 571 AN: 67968

Other (OTH) AF: 0.00803 AC: 17 AN: 2116

Alfa AF: 0.00281 Hom.: 949

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.75
DANN	Benign	0.25
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10169164; hg19: chr2-47478791;