NM_018235.3:c.*309C>T

Variant names:

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

Variant summary

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

The NM_018235.3(CNDP2):​c.*309C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.952 in 331,202 control chromosomes in the GnomAD database, including 151,755 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 0.91 (64618 hom., cov: 32)
  • Exomes 𝑓: 0.99 (87137 hom.)
• 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: 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 = 0.992 is higher than 0.05.

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>T		3_prime_UTR	Exon 12 of 12	NP_060705.2	Q96KP4-1
	CNDP2	NM_001370248.1		c.*309C>T		3_prime_UTR	Exon 12 of 12	NP_001357177.1	Q96KP4-1
	CNDP2	NM_001370249.1		c.*309C>T		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>T		3_prime_UTR	Exon 12 of 12	ENSP00000325548.4	Q96KP4-1
	CNDP2	ENST00000324301.12	TSL:1	c.*309C>T		3_prime_UTR	Exon 9 of 9	ENSP00000325756.8	Q96KP4-2
	CNDP2	ENST00000880651.1		c.*309C>T		3_prime_UTR	Exon 12 of 12	ENSP00000550710.1

Frequencies

GnomAD3 genomes AF: 0.913 AC: 138831 AN: 152122 Hom.: 64598 Cov.: 32

Gnomad AFR AF: 0.711

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.961

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 0.900

Gnomad SAS AF: 0.999

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.978

Gnomad NFE AF: 0.999

Gnomad OTH AF: 0.939

GnomAD4 exome AF: 0.986 AC: 176410 AN: 178962 Hom.: 87137 Cov.: 2 AF XY: 0.988 AC XY: 93927 AN XY: 95108

African (AFR) AF: 0.737 AC: 3596 AN: 4876

American (AMR) AF: 0.977 AC: 6543 AN: 6696

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 5370 AN: 5370

East Asian (EAS) AF: 0.914 AC: 7647 AN: 8364

South Asian (SAS) AF: 0.999 AC: 25324 AN: 25350

European-Finnish (FIN) AF: 1.00 AC: 9685 AN: 9686

Middle Eastern (MID) AF: 0.983 AC: 847 AN: 862

European-Non Finnish (NFE) AF: 0.999 AC: 107327 AN: 107424

Other (OTH) AF: 0.975 AC: 10071 AN: 10334

GnomAD4 genome AF: 0.912 AC: 138891 AN: 152240 Hom.: 64618 Cov.: 32 AF XY: 0.915 AC XY: 68089 AN XY: 74446

African (AFR) AF: 0.711 AC: 29482 AN: 41484

American (AMR) AF: 0.961 AC: 14709 AN: 15306

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 3470 AN: 3470

East Asian (EAS) AF: 0.900 AC: 4661 AN: 5178

South Asian (SAS) AF: 0.999 AC: 4826 AN: 4830

European-Finnish (FIN) AF: 1.00 AC: 10628 AN: 10628

Middle Eastern (MID) AF: 0.973 AC: 286 AN: 294

European-Non Finnish (NFE) AF: 0.999 AC: 67935 AN: 68024

Other (OTH) AF: 0.938 AC: 1982 AN: 2114

Alfa AF: 0.976 Hom.: 100418

Bravo AF: 0.900

Asia WGS AF: 0.945 AC: 3285 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	0.89
DANN	Benign	0.48
PhyloP100		-0.26
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
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: rs890336; hg19: chr18-72187612;