rs1896376

Variant names:

• chr10-123756313-C-T
• rs1896376
• NM_198148.3:c.1917+900G>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.1917+900G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0457 in 152,240 control chromosomes in the GnomAD database, including 200 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 0.046 (200 hom., cov: 34)
• Consequence: CPXM2 NM_198148.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0850
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.121 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPXM2	NM_198148.3	MANE Select	c.1917+900G>A		intron	N/A	NP_937791.2	Q8N436

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPXM2	ENST00000241305.4	TSL:1 MANE Select	c.1917+900G>A		intron	N/A	ENSP00000241305.3	Q8N436
	CPXM2	ENST00000909350.1		c.1914+900G>A		intron	N/A	ENSP00000579409.1
	CPXM2	ENST00000909348.1		c.1818+900G>A		intron	N/A	ENSP00000579407.1

Frequencies

GnomAD3 genomes AF: 0.0457 AC: 6959 AN: 152122 Hom.: 201 Cov.: 34

Gnomad AFR AF: 0.0105

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0793

Gnomad ASJ AF: 0.0585

Gnomad EAS AF: 0.0617

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.0431

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0522

Gnomad OTH AF: 0.0565

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

GnomAD4 genome AF: 0.0457 AC: 6958 AN: 152240 Hom.: 200 Cov.: 34 AF XY: 0.0477 AC XY: 3551 AN XY: 74432

African (AFR) AF: 0.0104 AC: 434 AN: 41540

American (AMR) AF: 0.0793 AC: 1213 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0585 AC: 203 AN: 3472

East Asian (EAS) AF: 0.0618 AC: 320 AN: 5174

South Asian (SAS) AF: 0.130 AC: 625 AN: 4822

European-Finnish (FIN) AF: 0.0431 AC: 457 AN: 10598

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0522 AC: 3550 AN: 68018

Other (OTH) AF: 0.0554 AC: 117 AN: 2112

Alfa AF: 0.0540 Hom.: 310

Bravo AF: 0.0469

Asia WGS AF: 0.0770 AC: 268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.72
PhyloP100		-0.085
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: rs1896376; hg19: chr10-125515829;