rs317711

Positions:

• chr7-29062692-C-G
• chr7-29062692-C-T

Variant summary

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

The NM_031311.5(CPVL):​c.1137+1369G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.78 in 152,136 control chromosomes in the GnomAD database, including 46,449 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 0.78 (46449 hom., cov: 31)
• Consequence: CPVL NM_031311.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.702

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=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.864 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CPVL	NM_031311.5	c.1137+1369G>C		intron_variant		ENST00000265394.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CPVL	ENST00000265394.10	c.1137+1369G>C		intron_variant		1	NM_031311.5	P1

Frequencies

GnomAD3 genomes AF: 0.780 AC: 118548 AN: 152018 Hom.: 46420 Cov.: 31

Gnomad AFR AF: 0.801

Gnomad AMI AF: 0.636

Gnomad AMR AF: 0.809

Gnomad ASJ AF: 0.786

Gnomad EAS AF: 0.863

Gnomad SAS AF: 0.886

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.749

Gnomad OTH AF: 0.774

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

GnomAD4 genome AF: 0.780 AC: 118632 AN: 152136 Hom.: 46449 Cov.: 31 AF XY: 0.785 AC XY: 58380 AN XY: 74360

Gnomad4 AFR AF: 0.800

Gnomad4 AMR AF: 0.809

Gnomad4 ASJ AF: 0.786

Gnomad4 EAS AF: 0.864

Gnomad4 SAS AF: 0.886

Gnomad4 FIN AF: 0.778

Gnomad4 NFE AF: 0.749

Gnomad4 OTH AF: 0.774

Alfa AF: 0.777 Hom.: 5713

Bravo AF: 0.780

Asia WGS AF: 0.856 AC: 2975 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.64
DANN	Benign	0.34

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: rs317711; hg19: chr7-29102308;