NM_198148.3:c.*827G>A

Variant names:

• chr10-123745937-C-T
• rs9060
• NM_198148.3:c.*827G>A

Variant summary

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

The NM_198148.3(CPXM2):​c.*827G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 151,622 control chromosomes in the GnomAD database, including 10,133 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 0.35 (10133 hom., cov: 31)
  • Exomes 𝑓: 0.27 (0 hom.)
• Consequence: CPXM2 NM_198148.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.744
• Publications: 6 publications found

Genes affected

CPXM2 (HGNC:26977): (carboxypeptidase X, M14 family member 2) Predicted to enable metallocarboxypeptidase activity. Predicted to be involved in peptide metabolic process and protein processing. Predicted to be active in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.509 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198148.3. 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
	CPXM2	NM_198148.3	MANE Select	c.*827G>A		3_prime_UTR	Exon 14 of 14	NP_937791.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPXM2	ENST00000241305.4	TSL:1 MANE Select	c.*827G>A		3_prime_UTR	Exon 14 of 14	ENSP00000241305.3
	CPXM2	ENST00000909350.1		c.*827G>A		3_prime_UTR	Exon 14 of 14	ENSP00000579409.1
	CPXM2	ENST00000909348.1		c.*827G>A		3_prime_UTR	Exon 13 of 13	ENSP00000579407.1

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52543 AN: 151474 Hom.: 10116 Cov.: 31

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.0619

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.349

GnomAD4 exome AF: 0.267 AC: 8 AN: 30 Hom.: 0 Cov.: 0 AF XY: 0.250 AC XY: 6 AN XY: 24

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.269 AC: 7 AN: 26

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.347 AC: 52603 AN: 151592 Hom.: 10133 Cov.: 31 AF XY: 0.342 AC XY: 25366 AN XY: 74076

African (AFR) AF: 0.515 AC: 21265 AN: 41268

American (AMR) AF: 0.290 AC: 4414 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1322 AN: 3470

East Asian (EAS) AF: 0.0620 AC: 317 AN: 5110

South Asian (SAS) AF: 0.332 AC: 1597 AN: 4808

European-Finnish (FIN) AF: 0.284 AC: 2979 AN: 10478

Middle Eastern (MID) AF: 0.394 AC: 115 AN: 292

European-Non Finnish (NFE) AF: 0.290 AC: 19683 AN: 67916

Other (OTH) AF: 0.345 AC: 727 AN: 2110

Alfa AF: 0.317 Hom.: 10139

Bravo AF: 0.353

Asia WGS AF: 0.212 AC: 737 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.72
DANN	Benign	0.28
PhyloP100		-0.74
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: rs9060; hg19: chr10-125505453;