ENST00000581272.5:c.-38+252G>C

Variant names:

• chr18-74496175-G-C
• rs12964619
• ENST00000581272.5:c.-38+252G>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000581272.5(CNDP2):​c.-38+252G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 34)
• Consequence: CNDP2 ENST00000581272.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.165
• Publications: 0 publications found

Genes affected

CNDP2 (HGNC:24437): (carnosine dipeptidase 2) CNDP2, also known as tissue carnosinase and peptidase A (EC 3.4.13.18), is a nonspecific dipeptidase rather than a selective carnosinase (Teufel et al., 2003 [PubMed 12473676]).[supplied by OMIM, Mar 2008]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000581272.5. 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
	CNDP2	NM_018235.3	MANE Select	c.-349G>C		upstream_gene	N/A	NP_060705.2
	CNDP2	NM_001370248.1		c.-294G>C		upstream_gene	N/A	NP_001357177.1
	CNDP2	NM_001370249.1		c.-616G>C		upstream_gene	N/A	NP_001357178.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNDP2	ENST00000581272.5	TSL:4	c.-38+252G>C		intron	N/A	ENSP00000464151.1
	CNDP2	ENST00000324262.9	TSL:1 MANE Select	c.-349G>C		upstream_gene	N/A	ENSP00000325548.4
	CNDP2	ENST00000579847.5	TSL:5	c.-294G>C		upstream_gene	N/A	ENSP00000462311.1

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	5.7
DANN	Benign	0.48
PhyloP100		0.17
PromoterAI		0.030	Neutral

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs12964619; hg19: chr18-72163410;