10-123843022-G-C

Position:

• chr10-123843022-G-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CPXM2	NM_198148.3	c.514-534C>G		intron_variant		ENST00000241305.4	NP_937791.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CPXM2	ENST00000241305.4	c.514-534C>G		intron_variant		1	NM_198148.3	ENSP00000241305	P1
CPXM2	ENST00000615851.4	c.-999-534C>G		intron_variant		5		ENSP00000483180
CPXM2	ENST00000368854.7	n.384-534C>G		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.428

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.409

Gnomad4 SAS AF: 0.346

Gnomad4 FIN AF: 0.179

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.302

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.85
DANN	Benign	0.43

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

Publications

LitVar

Other links and lift over

dbSNP: rs7071385; hg19: chr10-125602538;