rs236394

Variant names:

• chr6-36808967-T-A
• rs236394
• NM_020939.2:c.184-8897A>T

Your query was ambiguous. Multiple possible variants found:

• chr6-36808967-T-A
• chr6-36808967-T-G

Variant summary

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

The NM_020939.2(CPNE5):​c.184-8897A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.549 in 152,014 control chromosomes in the GnomAD database, including 24,079 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 0.55 (24079 hom., cov: 31)
• Consequence: CPNE5 NM_020939.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.549
• Publications: 3 publications found

Genes affected

CPNE5 (HGNC:2318): (copine 5) Calcium-dependent membrane-binding proteins may regulate molecular events at the interface of the cell membrane and cytoplasm. This gene is one of several genes that encode a calcium-dependent protein containing two N-terminal type II C2 domains and an integrin A domain-like sequence in the C-terminus. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene. More variants may exist, but their full-length natures could not be determined. [provided by RefSeq, Sep 2015]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.721 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020939.2. 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
	CPNE5	NM_020939.2	MANE Select	c.184-8897A>T		intron	N/A	NP_065990.1
	CPNE5	NM_001410887.1		c.184-8897A>T		intron	N/A	NP_001397816.1
	CPNE5	NM_001376889.1		c.184-8897A>T		intron	N/A	NP_001363818.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPNE5	ENST00000244751.7	TSL:1 MANE Select	c.184-8897A>T		intron	N/A	ENSP00000244751.2
	CPNE5	ENST00000633136.2	TSL:5	c.184-8897A>T		intron	N/A	ENSP00000487872.2
	CPNE5	ENST00000633280.1	TSL:5	c.184-8897A>T		intron	N/A	ENSP00000488125.1

Frequencies

GnomAD3 genomes AF: 0.549 AC: 83396 AN: 151896 Hom.: 24050 Cov.: 31

Gnomad AFR AF: 0.728

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.537

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.549 AC: 83471 AN: 152014 Hom.: 24079 Cov.: 31 AF XY: 0.543 AC XY: 40351 AN XY: 74298

African (AFR) AF: 0.728 AC: 30177 AN: 41460

American (AMR) AF: 0.539 AC: 8235 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1565 AN: 3470

East Asian (EAS) AF: 0.537 AC: 2769 AN: 5160

South Asian (SAS) AF: 0.421 AC: 2026 AN: 4816

European-Finnish (FIN) AF: 0.434 AC: 4585 AN: 10564

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.477 AC: 32415 AN: 67952

Other (OTH) AF: 0.528 AC: 1116 AN: 2114

Alfa AF: 0.376 Hom.: 994

Bravo AF: 0.574

Asia WGS AF: 0.467 AC: 1624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.0
DANN	Benign	0.82
PhyloP100		0.55
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: rs236394; hg19: chr6-36776743;