16-89582172-C-T

Position:

• chr16-89582172-C-T

Variant summary

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

The NM_153636.3(CPNE7):​c.358-1525C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 152,166 control chromosomes in the GnomAD database, including 13,098 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 0.38 (13098 hom., cov: 33)
• Consequence: CPNE7 NM_153636.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.21

Genes affected

CPNE7 (HGNC:2320): (copine 7) This gene encodes a member of the copine family, which is composed of calcium-dependent membrane-binding proteins. The gene product contains two N-terminal C2 domains and one von Willebrand factor A domain. The encoded protein may be involved in membrane trafficking. Two alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.508 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CPNE7	NM_153636.3	c.358-1525C>T		intron_variant		ENST00000319518.13	NP_705900.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CPNE7	ENST00000319518.13	c.358-1525C>T		intron_variant		1	NM_153636.3	ENSP00000317374.8
CPNE7	ENST00000268720.9	c.498-1272C>T		intron_variant		1		ENSP00000268720.5
CPNE7	ENST00000525982.5	n.358-1272C>T		intron_variant		5		ENSP00000431863.1

Frequencies

GnomAD3 genomes AF: 0.381 AC: 57889 AN: 152048 Hom.: 13105 Cov.: 33

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.380 AC: 57868 AN: 152166 Hom.: 13098 Cov.: 33 AF XY: 0.375 AC XY: 27879 AN XY: 74376

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.431

Gnomad4 ASJ AF: 0.585

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.366

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.513

Gnomad4 OTH AF: 0.476

Alfa AF: 0.499 Hom.: 26321

Bravo AF: 0.374

Asia WGS AF: 0.213 AC: 742 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.58
DANN	Benign	0.49

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

Publications

LitVar

Other links and lift over

dbSNP: rs352935; hg19: chr16-89648580;