21-32802930-C-A

Variant names:

• chr21-32802930-C-A
• rs4817502
• NM_001162495.3:c.-65+4712G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001162495.3(EPCIP):​c.-65+4712G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.717 in 152,048 control chromosomes in the GnomAD database, including 39,904 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 0.72 (39904 hom., cov: 31)
• Consequence: EPCIP NM_001162495.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.591
• Publications: 6 publications found

Genes affected

EPCIP (HGNC:1305): (exosomal polycystin 1 interacting protein)

EPCIP-AS1 (HGNC:1290): (EPCIP antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.887 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EPCIP	NM_001162495.3	c.-65+4712G>T		intron_variant	Intron 3 of 3	ENST00000479548.2	NP_001155967.2
EPCIP	NM_001162496.3	c.-64-8445G>T		intron_variant	Intron 1 of 1		NP_001155968.2
EPCIP	NM_019596.6	c.-65+7644G>T		intron_variant	Intron 2 of 2		NP_062542.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EPCIP	ENST00000479548.2	c.-65+4712G>T		intron_variant	Intron 3 of 3	1	NM_001162495.3	ENSP00000418653.1

Frequencies

GnomAD3 genomes AF: 0.717 AC: 108926 AN: 151930 Hom.: 39887 Cov.: 31

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.653

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.808

Gnomad EAS AF: 0.908

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.843

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.764

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.717 AC: 108993 AN: 152048 Hom.: 39904 Cov.: 31 AF XY: 0.721 AC XY: 53564 AN XY: 74332

African (AFR) AF: 0.562 AC: 23298 AN: 41428

American (AMR) AF: 0.767 AC: 11711 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.808 AC: 2805 AN: 3472

East Asian (EAS) AF: 0.908 AC: 4686 AN: 5158

South Asian (SAS) AF: 0.706 AC: 3401 AN: 4818

European-Finnish (FIN) AF: 0.843 AC: 8924 AN: 10586

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.764 AC: 51925 AN: 67998

Other (OTH) AF: 0.681 AC: 1440 AN: 2116

Alfa AF: 0.748 Hom.: 21415

Bravo AF: 0.708

Asia WGS AF: 0.749 AC: 2606 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.8
DANN	Benign	0.81
PhyloP100		0.59
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs4817502; hg19: chr21-34175240;