rs9470386

Variant names:

• chr6-36745943-G-A
• rs9470386
• NM_020939.2:c.1201-428C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-36745943-G-A
• chr6-36745943-G-C
• chr6-36745943-G-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.1201-428C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.44 in 152,024 control chromosomes in the GnomAD database, including 15,098 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 0.44 (15098 hom., cov: 32)
• Consequence: CPNE5 NM_020939.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.75
• Publications: 4 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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.499 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPNE5	NM_020939.2	MANE Select	c.1201-428C>T		intron	N/A	NP_065990.1
	CPNE5	NM_001410887.1		c.1252-428C>T		intron	N/A	NP_001397816.1
	CPNE5	NM_001376889.1		c.1252-428C>T		intron	N/A	NP_001363818.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPNE5	ENST00000244751.7	TSL:1 MANE Select	c.1201-428C>T		intron	N/A	ENSP00000244751.2
	CPNE5	ENST00000393189.2	TSL:1	c.325-428C>T		intron	N/A	ENSP00000376885.2
	CPNE5	ENST00000493411.2	TSL:1	n.381-428C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.440 AC: 66811 AN: 151904 Hom.: 15098 Cov.: 32

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.440 AC: 66851 AN: 152024 Hom.: 15098 Cov.: 32 AF XY: 0.432 AC XY: 32075 AN XY: 74308

African (AFR) AF: 0.393 AC: 16314 AN: 41460

American (AMR) AF: 0.388 AC: 5938 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.534 AC: 1853 AN: 3472

East Asian (EAS) AF: 0.293 AC: 1511 AN: 5158

South Asian (SAS) AF: 0.250 AC: 1205 AN: 4824

European-Finnish (FIN) AF: 0.415 AC: 4395 AN: 10578

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.504 AC: 34230 AN: 67928

Other (OTH) AF: 0.453 AC: 954 AN: 2104

Alfa AF: 0.479 Hom.: 33909

Bravo AF: 0.435

Asia WGS AF: 0.247 AC: 863 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.042
DANN	Benign	0.64
PhyloP100		-2.7
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: rs9470386; hg19: chr6-36713720;