chr18-74521136-A-G

Variant names:

• chr18-74521136-A-G
• rs890334
• NM_018235.3:c.*1068A>G

Variant summary

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

The NM_018235.3(CNDP2):​c.*1068A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.951 in 152,280 control chromosomes in the GnomAD database, including 69,175 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 0.95 (69160 hom., cov: 32)
  • Exomes 𝑓: 0.97 (15 hom.)
• Consequence: CNDP2 NM_018235.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68
• Publications: 4 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=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.99 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNDP2	NM_018235.3	MANE Select	c.*1068A>G		3_prime_UTR	Exon 12 of 12	NP_060705.2
	CNDP2	NM_001370248.1		c.*1068A>G		3_prime_UTR	Exon 12 of 12	NP_001357177.1
	CNDP2	NM_001370249.1		c.*1068A>G		3_prime_UTR	Exon 14 of 14	NP_001357178.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNDP2	ENST00000324262.9	TSL:1 MANE Select	c.*1068A>G		3_prime_UTR	Exon 12 of 12	ENSP00000325548.4
	CNDP2	ENST00000324301.12	TSL:1	c.*1068A>G		downstream_gene	N/A	ENSP00000325756.8
	CNDP2	ENST00000579847.5	TSL:5	c.*1068A>G		downstream_gene	N/A	ENSP00000462311.1

Frequencies

GnomAD3 genomes AF: 0.951 AC: 144665 AN: 152130 Hom.: 69118 Cov.: 32

Gnomad AFR AF: 0.854

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.974

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 0.901

Gnomad SAS AF: 1.00

Gnomad FIN AF: 0.985

Gnomad MID AF: 0.997

Gnomad NFE AF: 0.996

Gnomad OTH AF: 0.961

GnomAD4 exome AF: 0.969 AC: 31 AN: 32 Hom.: 15 Cov.: 0 AF XY: 0.950 AC XY: 19 AN XY: 20

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 14 AN: 14

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 10 AN: 10

Other (OTH) AF: 1.00 AC: 6 AN: 6

GnomAD4 genome AF: 0.951 AC: 144765 AN: 152248 Hom.: 69160 Cov.: 32 AF XY: 0.951 AC XY: 70789 AN XY: 74442

African (AFR) AF: 0.854 AC: 35443 AN: 41500

American (AMR) AF: 0.974 AC: 14903 AN: 15300

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 3472 AN: 3472

East Asian (EAS) AF: 0.901 AC: 4654 AN: 5164

South Asian (SAS) AF: 1.00 AC: 4828 AN: 4830

European-Finnish (FIN) AF: 0.985 AC: 10461 AN: 10622

Middle Eastern (MID) AF: 0.997 AC: 293 AN: 294

European-Non Finnish (NFE) AF: 0.996 AC: 67772 AN: 68042

Other (OTH) AF: 0.960 AC: 2027 AN: 2112

Alfa AF: 0.977 Hom.: 23850

Bravo AF: 0.946

Asia WGS AF: 0.956 AC: 3325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.11
DANN	Benign	0.12
PhyloP100		-1.7
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2
Mutation Taster		=97/3	polymorphism

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: rs890334; hg19: chr18-72188371;