dbSNP rs4817502: EPCIP:c.-65+4712G>T (chr21-32802930-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.591

Variant links:

Genes affected

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

EPCIP links:

C21orf62-AS1 (HGNC:1290): (EPCIP antisense RNA 1)

C21orf62-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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	Effect	Exon rank	MANE	Protein
EPCIP	NM_001162495.3 link	c.-65+4712G>T	intron_variant	Intron 3 of 3	ENST00000479548.2	NP_001155967.2
EPCIP	NM_001162496.3 link	c.-64-8445G>T	intron_variant	Intron 1 of 1		NP_001155968.2
EPCIP	NM_019596.6 link	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
C21orf62	ENST00000479548.2 link	c.-65+4712G>T		intron_variant	Intron 3 of 3	1	NM_001162495.3	ENSP00000418653.1		Q9NYP8

Frequencies

GnomAD3 genomes

AF:

0.717

AC:

108926

AN:

151930

Hom.:

39887

Cov.:

show subpopulations

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.:

AF XY:

0.721

AC XY:

53564

AN XY:

74332

show subpopulations

Gnomad4 AFR

AF:

0.562

Gnomad4 AMR

AF:

0.767

Gnomad4 ASJ

AF:

0.808

Gnomad4 EAS

AF:

0.908

Gnomad4 SAS

AF:

0.706

Gnomad4 FIN

AF:

0.843

Gnomad4 NFE

AF:

0.764

Gnomad4 OTH

AF:

0.681

Alfa

AF:

0.746

Hom.:

19135

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

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over