rs890334

chr18-74521136-A-Gchr18-74521136-A-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CNDP2	NM_018235.3	c.*1068A>G		3_prime_UTR_variant	12/12	ENST00000324262.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CNDP2	ENST00000324262.9	c.*1068A>G		3_prime_UTR_variant	12/12	1	NM_018235.3	P1

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

Gnomad4 EAS exome AF: 0.500

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 1.00

Gnomad4 OTH exome AF: 1.00

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

Gnomad4 AFR AF: 0.854

Gnomad4 AMR AF: 0.974

Gnomad4 ASJ AF: 1.00

Gnomad4 EAS AF: 0.901

Gnomad4 SAS AF: 1.00

Gnomad4 FIN AF: 0.985

Gnomad4 NFE AF: 0.996

Gnomad4 OTH AF: 0.960

Alfa AF: 0.978 Hom.: 13422

Bravo AF: 0.946

Asia WGS AF: 0.956 AC: 3325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.11
Dann	Benign	0.12
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs890334; hg19: chr18-72188371;