rs505532

chr7-29044776-T-C

Variant summary

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

The NM_031311.5(CPVL):c.1138-14017A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.646 in 152,114 control chromosomes in the GnomAD database, including 32,235 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 0.65 (32235 hom., cov: 32)
• Consequence: CPVL NM_031311.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141

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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CPVL	NM_031311.5	c.1138-14017A>G		intron_variant		ENST00000265394.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CPVL	ENST00000265394.10	c.1138-14017A>G		intron_variant		1	NM_031311.5	P1

Frequencies

GnomAD3 genomes AF: 0.646 AC: 98188 AN: 151996 Hom.: 32214 Cov.: 32

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.651

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.649

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

GnomAD4 genome AF: 0.646 AC: 98264 AN: 152114 Hom.: 32235 Cov.: 32 AF XY: 0.640 AC XY: 47573 AN XY: 74350

Gnomad4 AFR AF: 0.559

Gnomad4 AMR AF: 0.663

Gnomad4 ASJ AF: 0.654

Gnomad4 EAS AF: 0.415

Gnomad4 SAS AF: 0.619

Gnomad4 FIN AF: 0.670

Gnomad4 NFE AF: 0.712

Gnomad4 OTH AF: 0.646

Alfa AF: 0.692 Hom.: 57279

Bravo AF: 0.638

Asia WGS AF: 0.514 AC: 1789 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.2
Dann	Benign	0.59

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: rs505532; hg19: chr7-29084392;