rs2647952

Variant names:

• chr12-68925483-G-A
• rs2647952
• NM_198320.5:c.160+7195C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-68925483-G-A
• chr12-68925483-G-C

Variant summary

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

The NM_198320.5(CPM):​c.160+7195C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.769 in 152,138 control chromosomes in the GnomAD database, including 45,311 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 0.77 (45311 hom., cov: 33)
• Consequence: CPM NM_198320.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.192
• Publications: 2 publications found

Genes affected

CPM (HGNC:2311): (carboxypeptidase M) The protein encoded by this gene is a membrane-bound arginine/lysine carboxypeptidase. Its expression is associated with monocyte to macrophage differentiation. This encoded protein contains hydrophobic regions at the amino and carboxy termini and has 6 potential asparagine-linked glycosylation sites. The active site residues of carboxypeptidases A and B are conserved in this protein. Three alternatively spliced transcript variants encoding the same protein have been described for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.862 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CPM	NM_198320.5	c.160+7195C>T		intron_variant	Intron 2 of 8	ENST00000551568.6	NP_938079.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CPM	ENST00000551568.6	c.160+7195C>T		intron_variant	Intron 2 of 8	1	NM_198320.5	ENSP00000448517.1

Frequencies

GnomAD3 genomes AF: 0.769 AC: 116930 AN: 152020 Hom.: 45262 Cov.: 33

Gnomad AFR AF: 0.870

Gnomad AMI AF: 0.767

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.756

Gnomad EAS AF: 0.679

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.740

Gnomad OTH AF: 0.752

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

GnomAD4 genome AF: 0.769 AC: 117034 AN: 152138 Hom.: 45311 Cov.: 33 AF XY: 0.763 AC XY: 56755 AN XY: 74360

African (AFR) AF: 0.870 AC: 36132 AN: 41534

American (AMR) AF: 0.748 AC: 11426 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.756 AC: 2625 AN: 3470

East Asian (EAS) AF: 0.680 AC: 3518 AN: 5174

South Asian (SAS) AF: 0.744 AC: 3585 AN: 4818

European-Finnish (FIN) AF: 0.658 AC: 6953 AN: 10564

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.740 AC: 50314 AN: 67986

Other (OTH) AF: 0.750 AC: 1583 AN: 2110

Alfa AF: 0.768 Hom.: 7494

Bravo AF: 0.782

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.5
DANN	Benign	0.46
PhyloP100		0.19
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: rs2647952; hg19: chr12-69319263;