NM_001162495.3:c.-221+614A>G

Variant names:

• chr21-32812978-T-C
• rs10483014
• NM_001162495.3:c.-221+614A>G

Variant summary

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

The NM_001162495.3(EPCIP):​c.-221+614A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0737 in 152,278 control chromosomes in the GnomAD database, including 581 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 0.074 (581 hom., cov: 33)
• Consequence: EPCIP NM_001162495.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.895

Genes affected

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

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.111 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EPCIP	NM_001162495.3	c.-221+614A>G		intron_variant	Intron 1 of 3	ENST00000479548.2	NP_001155967.2
EPCIP	NM_001162496.3	c.-65+614A>G		intron_variant	Intron 1 of 1		NP_001155968.2
EPCIP	NM_019596.6	c.-146+614A>G		intron_variant	Intron 1 of 2		NP_062542.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C21orf62	ENST00000479548.2	c.-221+614A>G		intron_variant	Intron 1 of 3	1	NM_001162495.3	ENSP00000418653.1

Frequencies

GnomAD3 genomes AF: 0.0738 AC: 11228 AN: 152160 Hom.: 581 Cov.: 33

Gnomad AFR AF: 0.0212

Gnomad AMI AF: 0.0989

Gnomad AMR AF: 0.0798

Gnomad ASJ AF: 0.0671

Gnomad EAS AF: 0.00134

Gnomad SAS AF: 0.0296

Gnomad FIN AF: 0.0706

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.0879

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

GnomAD4 genome AF: 0.0737 AC: 11228 AN: 152278 Hom.: 581 Cov.: 33 AF XY: 0.0693 AC XY: 5164 AN XY: 74472

Gnomad4 AFR AF: 0.0211

Gnomad4 AMR AF: 0.0796

Gnomad4 ASJ AF: 0.0671

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0296

Gnomad4 FIN AF: 0.0706

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.0865

Alfa AF: 0.106 Hom.: 954

Bravo AF: 0.0724

Asia WGS AF: 0.0140 AC: 48 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10483014; hg19: chr21-34185288;