chr3-132243465-A-G

Variant names:

• chr3-132243465-A-G
• rs7622210
• ENST00000512055.5:c.-1829+40578T>C

Variant summary

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

The ENST00000512055.5(CPNE4):​c.-1829+40578T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 270,668 control chromosomes in the GnomAD database, including 3,904 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 0.17 (2813 hom., cov: 33)
  • Exomes 𝑓: 0.13 (1091 hom.)
• Consequence: CPNE4 ENST00000512055.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 5 publications found

Genes affected

CPNE4 (HGNC:2317): (copine 4) This gene belongs to the highly conserved copine family. It encodes a calcium-dependent, phospholipid-binding protein, which may be involved in membrane trafficking, mitogenesis and development. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]

RPL7P16 (HGNC:36591): (ribosomal protein L7 pseudogene 16)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000512055.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPNE4	ENST00000512055.5	TSL:2	c.-1829+40578T>C		intron	N/A	ENSP00000421705.1	Q96A23-1
	RPL7P16	ENST00000479738.1	TSL:6	n.*63T>C		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26404 AN: 152034 Hom.: 2800 Cov.: 33

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0880

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.0828

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.162

GnomAD4 exome AF: 0.130 AC: 15353 AN: 118516 Hom.: 1091 AF XY: 0.129 AC XY: 8487 AN XY: 66014

African (AFR) AF: 0.324 AC: 808 AN: 2490

American (AMR) AF: 0.0858 AC: 411 AN: 4790

Ashkenazi Jewish (ASJ) AF: 0.0952 AC: 285 AN: 2994

East Asian (EAS) AF: 0.195 AC: 909 AN: 4658

South Asian (SAS) AF: 0.116 AC: 2162 AN: 18686

European-Finnish (FIN) AF: 0.147 AC: 840 AN: 5724

Middle Eastern (MID) AF: 0.100 AC: 51 AN: 510

European-Non Finnish (NFE) AF: 0.125 AC: 9001 AN: 72010

Other (OTH) AF: 0.133 AC: 886 AN: 6654

GnomAD4 genome AF: 0.174 AC: 26447 AN: 152152 Hom.: 2813 Cov.: 33 AF XY: 0.173 AC XY: 12843 AN XY: 74382

African (AFR) AF: 0.305 AC: 12652 AN: 41480

American (AMR) AF: 0.106 AC: 1622 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0880 AC: 305 AN: 3466

East Asian (EAS) AF: 0.167 AC: 863 AN: 5170

South Asian (SAS) AF: 0.107 AC: 516 AN: 4824

European-Finnish (FIN) AF: 0.161 AC: 1709 AN: 10588

Middle Eastern (MID) AF: 0.0788 AC: 23 AN: 292

European-Non Finnish (NFE) AF: 0.122 AC: 8283 AN: 68012

Other (OTH) AF: 0.162 AC: 343 AN: 2112

Alfa AF: 0.135 Hom.: 782

Bravo AF: 0.176

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.26
DANN	Benign	0.75
PhyloP100		-1.3
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7622210; hg19: chr3-131962309;