NM_198320.5:c.160+17081T>C

Variant names:

• chr12-68915597-A-G
• rs1144961
• NM_198320.5:c.160+17081T>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+17081T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.781 in 152,194 control chromosomes in the GnomAD database, including 46,898 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 0.78 (46898 hom., cov: 33)
• Consequence: CPM NM_198320.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 1 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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.896 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CPM	NM_198320.5	c.160+17081T>C		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+17081T>C		intron_variant	Intron 2 of 8	1	NM_198320.5	ENSP00000448517.1

Frequencies

GnomAD3 genomes AF: 0.781 AC: 118784 AN: 152076 Hom.: 46838 Cov.: 33

Gnomad AFR AF: 0.903

Gnomad AMI AF: 0.763

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.760

Gnomad EAS AF: 0.671

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.744

Gnomad OTH AF: 0.763

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

GnomAD4 genome AF: 0.781 AC: 118901 AN: 152194 Hom.: 46898 Cov.: 33 AF XY: 0.775 AC XY: 57612 AN XY: 74368

African (AFR) AF: 0.903 AC: 37539 AN: 41554

American (AMR) AF: 0.757 AC: 11572 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.760 AC: 2637 AN: 3470

East Asian (EAS) AF: 0.671 AC: 3474 AN: 5174

South Asian (SAS) AF: 0.751 AC: 3620 AN: 4822

European-Finnish (FIN) AF: 0.656 AC: 6919 AN: 10550

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.744 AC: 50628 AN: 68016

Other (OTH) AF: 0.762 AC: 1610 AN: 2114

Alfa AF: 0.745 Hom.: 21870

Bravo AF: 0.796

Asia WGS AF: 0.677 AC: 2358 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.6
DANN	Benign	0.69
PhyloP100		0.35
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: rs1144961; hg19: chr12-69309377;