2-47251652-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NR_110208.1(EPCAM-DT):n.404-52109A>C variant causes a intron, non coding transcript 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 NR_110208.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 10 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EPCAM-DT	NR_110208.1	n.404-52109A>C		intron_variant, non_coding_transcript_variant
EPCAM-DT	NR_110207.1	n.175-30329A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EPCAM-DT	ENST00000448713.5	n.165-58835A>C		intron_variant, non_coding_transcript_variant		4
EPCAM-DT	ENST00000419035.1	n.67-30329A>C		intron_variant, non_coding_transcript_variant		2
EPCAM-DT	ENST00000441997.5	n.404-52109A>C		intron_variant, non_coding_transcript_variant		4
EPCAM-DT	ENST00000658129.1	n.43-30329A>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.00157

Gnomad4 AMR AF: 0.00511

Gnomad4 ASJ AF: 0.00923

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0322

Gnomad4 FIN AF: 0.00247

Gnomad4 NFE AF: 0.00840

Gnomad4 OTH AF: 0.00803

Alfa AF: 0.00281 Hom.: 949

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.75
Dann	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10169164; hg19: chr2-47478791;