ENST00000419035.1:n.67-33179T>C

Variant names:

• chr2-47254502-A-G
• rs10190105
• ENST00000419035.1:n.67-33179T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000419035.1(EPCAM-DT):​n.67-33179T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,114 control chromosomes in the GnomAD database, including 3,039 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 0.18 (3039 hom., cov: 32)
• Consequence: EPCAM-DT ENST00000419035.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80

Genes affected

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

LOC107985882 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.53 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EPCAM-DT	NR_110207.1	n.175-33179T>C		intron_variant	Intron 1 of 2
EPCAM-DT	NR_110208.1	n.404-54959T>C		intron_variant	Intron 3 of 4
LOC107985882	XR_001739451.1	n.606-1617T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EPCAM-DT	ENST00000419035.1	n.67-33179T>C		intron_variant	Intron 1 of 2	2
EPCAM-DT	ENST00000441997.5	n.404-54959T>C		intron_variant	Intron 3 of 4	4
EPCAM-DT	ENST00000448713.5	n.165-61685T>C		intron_variant	Intron 2 of 2	4
EPCAM-DT	ENST00000658129.1	n.43-33179T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27559 AN: 151996 Hom.: 3040 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.165

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.0922

Gnomad EAS AF: 0.548

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.181 AC: 27573 AN: 152114 Hom.: 3039 Cov.: 32 AF XY: 0.187 AC XY: 13870 AN XY: 74364

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.0922

Gnomad4 EAS AF: 0.547

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.256

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.165

Alfa AF: 0.188 Hom.: 338

Bravo AF: 0.173

Asia WGS AF: 0.313 AC: 1088 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.79
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10190105; hg19: chr2-47481641;