18-74513508-G-A

Position:

• chr18-74513508-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018235.3(CNDP2):​c.743-51G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0313 in 1,553,184 control chromosomes in the GnomAD database, including 1,910 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 0.069 (782 hom., cov: 33)
  • Exomes 𝑓: 0.027 (1128 hom.)
• Consequence: CNDP2 NM_018235.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CNDP2	NM_018235.3	c.743-51G>A		intron_variant		ENST00000324262.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CNDP2	ENST00000324262.9	c.743-51G>A		intron_variant		1	NM_018235.3	P1

Frequencies

GnomAD3 genomes AF: 0.0690 AC: 10498 AN: 152188 Hom.: 780 Cov.: 33

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0325

Gnomad ASJ AF: 0.0533

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0577

Gnomad FIN AF: 0.0128

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0220

Gnomad OTH AF: 0.0549

GnomAD3 exomes AF: 0.0365 AC: 6779 AN: 185968 Hom.: 356 AF XY: 0.0349 AC XY: 3494 AN XY: 99998

Gnomad AFR exome AF: 0.190

Gnomad AMR exome AF: 0.0177

Gnomad ASJ exome AF: 0.0555

Gnomad EAS exome AF: 0.000633

Gnomad SAS exome AF: 0.0600

Gnomad FIN exome AF: 0.0139

Gnomad NFE exome AF: 0.0220

Gnomad OTH exome AF: 0.0325

GnomAD4 exome AF: 0.0272 AC: 38105 AN: 1400878 Hom.: 1128 Cov.: 29 AF XY: 0.0278 AC XY: 19261 AN XY: 691946

Gnomad4 AFR exome AF: 0.192

Gnomad4 AMR exome AF: 0.0200

Gnomad4 ASJ exome AF: 0.0598

Gnomad4 EAS exome AF: 0.000208

Gnomad4 SAS exome AF: 0.0568

Gnomad4 FIN exome AF: 0.0149

Gnomad4 NFE exome AF: 0.0206

Gnomad4 OTH exome AF: 0.0356

GnomAD4 genome AF: 0.0690 AC: 10512 AN: 152306 Hom.: 782 Cov.: 33 AF XY: 0.0679 AC XY: 5056 AN XY: 74476

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.0325

Gnomad4 ASJ AF: 0.0533

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.0577

Gnomad4 FIN AF: 0.0128

Gnomad4 NFE AF: 0.0220

Gnomad4 OTH AF: 0.0539

Alfa AF: 0.0233 Hom.: 38

Bravo AF: 0.0758

Asia WGS AF: 0.0270 AC: 92 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.63
DANN	Benign	0.50
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs8090744; hg19: chr18-72180743;