21-32802930-C-G

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001162495.3(EPCIP):​c.-65+4712G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001162495.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EPCIP	NM_001162495.3	MANE Select	c.-65+4712G>C		intron	N/A	NP_001155967.2	Q9NYP8
	EPCIP	NM_001162496.3		c.-64-8445G>C		intron	N/A	NP_001155968.2	Q9NYP8
	EPCIP	NM_019596.6		c.-65+7644G>C		intron	N/A	NP_062542.5	Q9NYP8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EPCIP	ENST00000479548.2	TSL:1 MANE Select	c.-65+4712G>C		intron	N/A	ENSP00000418653.1	Q9NYP8
	EPCIP	ENST00000487113.1	TSL:1	c.-64-8445G>C		intron	N/A	ENSP00000418511.1	Q9NYP8
	EPCIP	ENST00000490358.5	TSL:1	c.-65+7644G>C		intron	N/A	ENSP00000418830.1	Q9NYP8

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.6
DANN	Benign	0.72
PhyloP100		0.59

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;