rs7071385

Variant names:

• chr10-123843022-G-C
• rs7071385
• NM_198148.3:c.514-534C>G

Variant summary

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

The NM_198148.3(CPXM2):​c.514-534C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 152,072 control chromosomes in the GnomAD database, including 7,479 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 0.30 (7479 hom., cov: 32)
• Consequence: CPXM2 NM_198148.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.607
• Publications: 0 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.423 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.514-534C>G		intron	N/A	NP_937791.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPXM2	ENST00000241305.4	TSL:1 MANE Select	c.514-534C>G		intron	N/A	ENSP00000241305.3
	CPXM2	ENST00000615851.4	TSL:5	c.-999-534C>G		intron	N/A	ENSP00000483180.1
	CPXM2	ENST00000368854.7	TSL:2	n.384-534C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45622 AN: 151954 Hom.: 7468 Cov.: 32

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.300 AC: 45676 AN: 152072 Hom.: 7479 Cov.: 32 AF XY: 0.299 AC XY: 22227 AN XY: 74320

African (AFR) AF: 0.428 AC: 17741 AN: 41462

American (AMR) AF: 0.287 AC: 4390 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 1153 AN: 3472

East Asian (EAS) AF: 0.409 AC: 2116 AN: 5170

South Asian (SAS) AF: 0.346 AC: 1669 AN: 4822

European-Finnish (FIN) AF: 0.179 AC: 1895 AN: 10570

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15789 AN: 67978

Other (OTH) AF: 0.302 AC: 638 AN: 2112

Alfa AF: 0.279 Hom.: 707

Bravo AF: 0.314

Asia WGS AF: 0.390 AC: 1356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.85
DANN	Benign	0.43
PhyloP100		-0.61
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: rs7071385; hg19: chr10-125602538;