7-29124008-T-G

Position:

• chr7-29124008-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.-10-2937A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.906 in 152,136 control chromosomes in the GnomAD database, including 62,680 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 0.91 (62680 hom., cov: 31)
• Consequence: CPVL NM_031311.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.44

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]

CPVL (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CPVL	NM_031311.5	c.-10-2937A>C		intron_variant		ENST00000265394.10	NP_112601.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CPVL	ENST00000265394.10	c.-10-2937A>C		intron_variant		1	NM_031311.5	ENSP00000265394.5

Frequencies

GnomAD3 genomes AF: 0.906 AC: 137747 AN: 152018 Hom.: 62614 Cov.: 31

Gnomad AFR AF: 0.976

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.914

Gnomad ASJ AF: 0.831

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.951

Gnomad FIN AF: 0.903

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.858

Gnomad OTH AF: 0.883

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

GnomAD4 genome AF: 0.906 AC: 137874 AN: 152136 Hom.: 62680 Cov.: 31 AF XY: 0.910 AC XY: 67664 AN XY: 74368

Gnomad4 AFR AF: 0.976

Gnomad4 AMR AF: 0.914

Gnomad4 ASJ AF: 0.831

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.951

Gnomad4 FIN AF: 0.903

Gnomad4 NFE AF: 0.858

Gnomad4 OTH AF: 0.885

Alfa AF: 0.865 Hom.: 68196

Bravo AF: 0.908

Asia WGS AF: 0.976 AC: 3392 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.5
DANN	Benign	0.70

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: rs245857; hg19: chr7-29163624;