chr7-29026702-T-G

Variant names:

• chr7-29026702-T-G
• rs506511
• NM_031311.5:c.1320+3875A>C

Variant summary

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

The NM_031311.5(CPVL):​c.1320+3875A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 151,998 control chromosomes in the GnomAD database, including 13,299 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 0.40 (13299 hom., cov: 32)
• Consequence: CPVL NM_031311.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.267
• Publications: 4 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031311.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPVL	NM_031311.5	MANE Select	c.1320+3875A>C		intron	N/A	NP_112601.3
	CPVL	NM_001371264.1		c.1362+3875A>C		intron	N/A	NP_001358193.1
	CPVL	NM_001348052.1		c.1320+3875A>C		intron	N/A	NP_001334981.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPVL	ENST00000265394.10	TSL:1 MANE Select	c.1320+3875A>C		intron	N/A	ENSP00000265394.5
	CPVL	ENST00000396276.7	TSL:1	c.1320+3875A>C		intron	N/A	ENSP00000379572.3
	CPVL	ENST00000409850.5	TSL:2	c.1320+3875A>C		intron	N/A	ENSP00000387164.1

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61356 AN: 151880 Hom.: 13293 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.404 AC: 61390 AN: 151998 Hom.: 13299 Cov.: 32 AF XY: 0.397 AC XY: 29481 AN XY: 74278

African (AFR) AF: 0.286 AC: 11856 AN: 41478

American (AMR) AF: 0.387 AC: 5920 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.435 AC: 1508 AN: 3470

East Asian (EAS) AF: 0.136 AC: 705 AN: 5180

South Asian (SAS) AF: 0.388 AC: 1870 AN: 4820

European-Finnish (FIN) AF: 0.400 AC: 4218 AN: 10540

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.501 AC: 34051 AN: 67912

Other (OTH) AF: 0.412 AC: 871 AN: 2112

Alfa AF: 0.437 Hom.: 2620

Bravo AF: 0.396

Asia WGS AF: 0.246 AC: 857 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.5
DANN	Benign	0.79
PhyloP100		0.27
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: rs506511; hg19: chr7-29066318;