rs506511

chr7-29026702-T-G

Variant summary

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

The NM_031311.5(CPVL):c.1320+3875A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 151,998 control chromosomes in the GnomAD database, including 13,299 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 0.40 (13299 hom., cov: 32)
• Consequence: CPVL NM_031311.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.267

Genes affected

CPVL (HGNC:14399): (carboxypeptidase vitellogenic like) The protein encoded by this gene is a carboxypeptidase and bears strong sequence similarity to serine carboxypeptidases. Carboxypeptidases are a large class of proteases that act to cleave a single amino acid from the carboxy termini of proteins or peptides. The exact function of this protein, however, has not been determined. [provided by RefSeq, Jan 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CPVL	NM_031311.5	c.1320+3875A>C		intron_variant		ENST00000265394.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CPVL	ENST00000265394.10	c.1320+3875A>C		intron_variant		1	NM_031311.5	P1

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61356 AN: 151880 Hom.: 13293 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.404 AC: 61390 AN: 151998 Hom.: 13299 Cov.: 32 AF XY: 0.397 AC XY: 29481 AN XY: 74278

Gnomad4 AFR AF: 0.286

Gnomad4 AMR AF: 0.387

Gnomad4 ASJ AF: 0.435

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.400

Gnomad4 NFE AF: 0.501

Gnomad4 OTH AF: 0.412

Alfa AF: 0.442 Hom.: 2593

Bravo AF: 0.396

Asia WGS AF: 0.246 AC: 857 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	3.5
Dann	Benign	0.79

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: rs506511; hg19: chr7-29066318;