rs10486607

chr7-29144873-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.-11+1556G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 152,132 control chromosomes in the GnomAD database, including 1,064 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 0.11 (1064 hom., cov: 31)
• Consequence: CPVL NM_031311.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.348

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CPVL	NM_031311.5	c.-11+1556G>A		intron_variant		ENST00000265394.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CPVL	ENST00000265394.10	c.-11+1556G>A		intron_variant		1	NM_031311.5	P1
	ENST00000578605.1	n.191-981C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17116 AN: 152016 Hom.: 1064 Cov.: 31

Gnomad AFR AF: 0.0653

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.0362

Gnomad SAS AF: 0.0808

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.113 AC: 17120 AN: 152132 Hom.: 1064 Cov.: 31 AF XY: 0.112 AC XY: 8358 AN XY: 74368

Gnomad4 AFR AF: 0.0652

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.0361

Gnomad4 SAS AF: 0.0805

Gnomad4 FIN AF: 0.184

Gnomad4 NFE AF: 0.136

Gnomad4 OTH AF: 0.135

Alfa AF: 0.131 Hom.: 3156

Bravo AF: 0.105

Asia WGS AF: 0.0690 AC: 239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	4.3
Dann	Benign	0.39

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: rs10486607; hg19: chr7-29184489;