chr7-29001574-T-C

Variant names:

• chr7-29001574-T-C
• rs2252521
• NM_031311.5:c.1321-5692A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_031311.5(CPVL):​c.1321-5692A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.63 in 152,050 control chromosomes in the GnomAD database, including 31,522 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 0.63 (31522 hom., cov: 32)
• Consequence: CPVL NM_031311.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338
• Publications: 15 publications found

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-AS2 (HGNC:56138): (CPVL antisense RNA 2)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.718 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CPVL	NM_031311.5	c.1321-5692A>G		intron_variant	Intron 12 of 12	ENST00000265394.10	NP_112601.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CPVL	ENST00000265394.10	c.1321-5692A>G		intron_variant	Intron 12 of 12	1	NM_031311.5	ENSP00000265394.5

Frequencies

GnomAD3 genomes AF: 0.630 AC: 95721 AN: 151932 Hom.: 31503 Cov.: 32

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.736

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.704

Gnomad FIN AF: 0.755

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.630 AC: 95793 AN: 152050 Hom.: 31522 Cov.: 32 AF XY: 0.632 AC XY: 46948 AN XY: 74308

African (AFR) AF: 0.434 AC: 17984 AN: 41440

American (AMR) AF: 0.662 AC: 10117 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.736 AC: 2550 AN: 3466

East Asian (EAS) AF: 0.494 AC: 2550 AN: 5162

South Asian (SAS) AF: 0.705 AC: 3392 AN: 4812

European-Finnish (FIN) AF: 0.755 AC: 7985 AN: 10572

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.724 AC: 49225 AN: 68008

Other (OTH) AF: 0.649 AC: 1371 AN: 2112

Alfa AF: 0.690 Hom.: 158585

Bravo AF: 0.610

Asia WGS AF: 0.592 AC: 2057 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.4
DANN	Benign	0.43
PhyloP100		-0.34
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2252521; hg19: chr7-29041190;