2-47224689-G-C

Position:

• chr2-47224689-G-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

EPCAM-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EPCAM-DT	NR_110207.1	n.175-3366C>G		intron_variant
EPCAM-DT	NR_110208.1	n.404-25146C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EPCAM-DT	ENST00000419035.1	n.67-3366C>G		intron_variant		2
EPCAM-DT	ENST00000441997.5	n.404-25146C>G		intron_variant		4
EPCAM-DT	ENST00000448713.5	n.165-31872C>G		intron_variant		4
EPCAM-DT	ENST00000658129.1	n.43-3366C>G		intron_variant

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

Gnomad4 AFR AF: 0.818

Gnomad4 AMR AF: 0.290

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.288

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.226

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.371

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12612040; hg19: chr2-47451828;