NM_018235.3:c.*309C>G

Variant names:

• chr18-74520377-C-G
• rs890336
• NM_018235.3:c.*309C>G

Variant summary

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

The NM_018235.3(CNDP2):​c.*309C>G variant causes a 3 prime UTR 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: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CNDP2 NM_018235.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.258
• Publications: 9 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=-0.91).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018235.3. 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
	CNDP2	NM_018235.3	MANE Select	c.*309C>G		3_prime_UTR	Exon 12 of 12	NP_060705.2	Q96KP4-1
	CNDP2	NM_001370248.1		c.*309C>G		3_prime_UTR	Exon 12 of 12	NP_001357177.1	Q96KP4-1
	CNDP2	NM_001370249.1		c.*309C>G		3_prime_UTR	Exon 14 of 14	NP_001357178.1	Q96KP4-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNDP2	ENST00000324262.9	TSL:1 MANE Select	c.*309C>G		3_prime_UTR	Exon 12 of 12	ENSP00000325548.4	Q96KP4-1
	CNDP2	ENST00000324301.12	TSL:1	c.*309C>G		3_prime_UTR	Exon 9 of 9	ENSP00000325756.8	Q96KP4-2
	CNDP2	ENST00000880651.1		c.*309C>G		3_prime_UTR	Exon 12 of 12	ENSP00000550710.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 179006 Hom.: 0 Cov.: 2 AF XY: 0.00 AC XY: 0 AN XY: 95132

African (AFR) AF: 0.00 AC: 0 AN: 4896

American (AMR) AF: 0.00 AC: 0 AN: 6696

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 5370

East Asian (EAS) AF: 0.00 AC: 0 AN: 8376

South Asian (SAS) AF: 0.00 AC: 0 AN: 25350

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 9686

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 864

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 107426

Other (OTH) AF: 0.00 AC: 0 AN: 10342

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 100418

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.64
DANN	Benign	0.34
PhyloP100		-0.26

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: rs890336; hg19: chr18-72187612;