rs2154427

Variant names:

• chr21-32796263-G-A
• rs2154427
• NM_001162495.3:c.-64-1778C>T

Your query was ambiguous. Multiple possible variants found:

• chr21-32796263-G-A
• chr21-32796263-G-C

Variant summary

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

The NM_001162495.3(EPCIP):​c.-64-1778C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,234 control chromosomes in the GnomAD database, including 987 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 0.11 (987 hom., cov: 32)
• Consequence: EPCIP NM_001162495.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.127
• Publications: 8 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EPCIP	NM_001162495.3	MANE Select	c.-64-1778C>T		intron	N/A	NP_001155967.2
	EPCIP	NM_001162496.3		c.-64-1778C>T		intron	N/A	NP_001155968.2
	EPCIP	NM_019596.6		c.-64-1778C>T		intron	N/A	NP_062542.5

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EPCIP	ENST00000479548.2	TSL:1 MANE Select	c.-64-1778C>T		intron	N/A	ENSP00000418653.1
	EPCIP	ENST00000487113.1	TSL:1	c.-64-1778C>T		intron	N/A	ENSP00000418511.1
	EPCIP	ENST00000490358.5	TSL:1	c.-64-1778C>T		intron	N/A	ENSP00000418830.1

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16500 AN: 152114 Hom.: 985 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.0792

Gnomad EAS AF: 0.00829

Gnomad SAS AF: 0.0725

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.109 AC: 16521 AN: 152234 Hom.: 987 Cov.: 32 AF XY: 0.108 AC XY: 8009 AN XY: 74438

African (AFR) AF: 0.134 AC: 5576 AN: 41542

American (AMR) AF: 0.108 AC: 1659 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0792 AC: 275 AN: 3472

East Asian (EAS) AF: 0.00831 AC: 43 AN: 5174

South Asian (SAS) AF: 0.0726 AC: 350 AN: 4824

European-Finnish (FIN) AF: 0.104 AC: 1099 AN: 10598

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7153 AN: 68010

Other (OTH) AF: 0.124 AC: 262 AN: 2116

Alfa AF: 0.100 Hom.: 1096

Bravo AF: 0.109

Asia WGS AF: 0.0420 AC: 145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.2
DANN	Benign	0.88
PhyloP100		-0.13
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: rs2154427; hg19: chr21-34168573;