rs505532

Variant names:

• chr7-29044776-T-C
• rs505532
• NM_031311.5:c.1138-14017A>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.1138-14017A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.646 in 152,114 control chromosomes in the GnomAD database, including 32,235 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 0.65 (32235 hom., cov: 32)
• Consequence: CPVL NM_031311.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141
• Publications: 8 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CPVL	NM_031311.5	c.1138-14017A>G		intron_variant	Intron 11 of 12	ENST00000265394.10	NP_112601.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CPVL	ENST00000265394.10	c.1138-14017A>G		intron_variant	Intron 11 of 12	1	NM_031311.5	ENSP00000265394.5

Frequencies

GnomAD3 genomes AF: 0.646 AC: 98188 AN: 151996 Hom.: 32214 Cov.: 32

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.651

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.649

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

GnomAD4 genome AF: 0.646 AC: 98264 AN: 152114 Hom.: 32235 Cov.: 32 AF XY: 0.640 AC XY: 47573 AN XY: 74350

African (AFR) AF: 0.559 AC: 23207 AN: 41496

American (AMR) AF: 0.663 AC: 10139 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.654 AC: 2271 AN: 3470

East Asian (EAS) AF: 0.415 AC: 2145 AN: 5168

South Asian (SAS) AF: 0.619 AC: 2982 AN: 4818

European-Finnish (FIN) AF: 0.670 AC: 7076 AN: 10564

Middle Eastern (MID) AF: 0.648 AC: 188 AN: 290

European-Non Finnish (NFE) AF: 0.712 AC: 48391 AN: 68000

Other (OTH) AF: 0.646 AC: 1365 AN: 2112

Alfa AF: 0.684 Hom.: 94903

Bravo AF: 0.638

Asia WGS AF: 0.514 AC: 1789 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.2
DANN	Benign	0.59
PhyloP100		-0.14
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: rs505532; hg19: chr7-29084392;