rs9470387

Variant names:

• chr6-36746081-C-A
• rs9470387
• NM_020939.2:c.1200+315G>T

Variant summary

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

The NM_020939.2(CPNE5):​c.1200+315G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 797,838 control chromosomes in the GnomAD database, including 39,644 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 0.27 (5735 hom., cov: 32)
  • Exomes 𝑓: 0.32 (33909 hom.)
• Consequence: CPNE5 NM_020939.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890
• Publications: 2 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=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CPNE5	NM_020939.2	c.1200+315G>T		intron_variant	Intron 16 of 20	ENST00000244751.7	NP_065990.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CPNE5	ENST00000244751.7	c.1200+315G>T		intron_variant	Intron 16 of 20	1	NM_020939.2	ENSP00000244751.2

Frequencies

GnomAD3 genomes AF: 0.270 AC: 41068 AN: 151902 Hom.: 5736 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.249

GnomAD4 exome AF: 0.322 AC: 207982 AN: 645818 Hom.: 33909 AF XY: 0.321 AC XY: 96751 AN XY: 301702

African (AFR) AF: 0.236 AC: 2821 AN: 11948

American (AMR) AF: 0.173 AC: 130 AN: 752

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 1123 AN: 4080

East Asian (EAS) AF: 0.209 AC: 586 AN: 2800

South Asian (SAS) AF: 0.208 AC: 2670 AN: 12820

European-Finnish (FIN) AF: 0.278 AC: 60 AN: 216

Middle Eastern (MID) AF: 0.241 AC: 308 AN: 1276

European-Non Finnish (NFE) AF: 0.328 AC: 194078 AN: 590862

Other (OTH) AF: 0.295 AC: 6206 AN: 21064

GnomAD4 genome AF: 0.270 AC: 41095 AN: 152020 Hom.: 5735 Cov.: 32 AF XY: 0.264 AC XY: 19614 AN XY: 74304

African (AFR) AF: 0.241 AC: 9993 AN: 41452

American (AMR) AF: 0.189 AC: 2895 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.294 AC: 1021 AN: 3468

East Asian (EAS) AF: 0.207 AC: 1064 AN: 5152

South Asian (SAS) AF: 0.197 AC: 953 AN: 4828

European-Finnish (FIN) AF: 0.254 AC: 2688 AN: 10578

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.319 AC: 21651 AN: 67950

Other (OTH) AF: 0.246 AC: 519 AN: 2108

Alfa AF: 0.295 Hom.: 18973

Bravo AF: 0.262

Asia WGS AF: 0.174 AC: 603 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.6
DANN	Benign	0.88
PhyloP100		0.089
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: rs9470387; hg19: chr6-36713858;