18-74511065-G-T

Position:

• chr18-74511065-G-T

Variant summary

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

The NM_018235.3(CNDP2):​c.657+52G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 1,501,194 control chromosomes in the GnomAD database, including 29,718 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 0.18 (2652 hom., cov: 32)
  • Exomes 𝑓: 0.20 (27066 hom.)
• Consequence: CNDP2 NM_018235.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.256

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CNDP2	NM_018235.3	c.657+52G>T		intron_variant		ENST00000324262.9	NP_060705.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CNDP2	ENST00000324262.9	c.657+52G>T		intron_variant		1	NM_018235.3	ENSP00000325548	P1

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26711 AN: 151960 Hom.: 2644 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.191

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.186

GnomAD3 exomes AF: 0.205 AC: 41036 AN: 200454 Hom.: 4592 AF XY: 0.204 AC XY: 21934 AN XY: 107416

Gnomad AFR exome AF: 0.110

Gnomad AMR exome AF: 0.327

Gnomad ASJ exome AF: 0.145

Gnomad EAS exome AF: 0.294

Gnomad SAS exome AF: 0.223

Gnomad FIN exome AF: 0.113

Gnomad NFE exome AF: 0.185

Gnomad OTH exome AF: 0.190

GnomAD4 exome AF: 0.196 AC: 264045 AN: 1349116 Hom.: 27066 Cov.: 19 AF XY: 0.197 AC XY: 131829 AN XY: 670706

Gnomad4 AFR exome AF: 0.106

Gnomad4 AMR exome AF: 0.324

Gnomad4 ASJ exome AF: 0.144

Gnomad4 EAS exome AF: 0.294

Gnomad4 SAS exome AF: 0.228

Gnomad4 FIN exome AF: 0.119

Gnomad4 NFE exome AF: 0.193

Gnomad4 OTH exome AF: 0.183

GnomAD4 genome AF: 0.176 AC: 26723 AN: 152078 Hom.: 2652 Cov.: 32 AF XY: 0.178 AC XY: 13201 AN XY: 74362

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.280

Gnomad4 ASJ AF: 0.155

Gnomad4 EAS AF: 0.289

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.185

Alfa AF: 0.128 Hom.: 345

Bravo AF: 0.184

Asia WGS AF: 0.270 AC: 943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	11
DANN	Benign	0.77

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.14		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: rs2278158; hg19: chr18-72178300; COSMIC: COSV60839280; COSMIC: COSV60839280;