rs2241511

Variant names:

• chr18-74513488-G-A
• rs2241511
• NM_018235.3:c.743-71G>A

Variant summary

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

The NM_018235.3(CNDP2):​c.743-71G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 1,452,442 control chromosomes in the GnomAD database, including 148,222 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 0.43 (14210 hom., cov: 34)
  • Exomes 𝑓: 0.45 (134012 hom.)
• Consequence: CNDP2 NM_018235.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.846
• Publications: 10 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNDP2	NM_018235.3	c.743-71G>A		intron_variant	Intron 7 of 11	ENST00000324262.9	NP_060705.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNDP2	ENST00000324262.9	c.743-71G>A		intron_variant	Intron 7 of 11	1	NM_018235.3	ENSP00000325548.4

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64813 AN: 152014 Hom.: 14200 Cov.: 34

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.665

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.427

GnomAD4 exome AF: 0.451 AC: 587035 AN: 1300310 Hom.: 134012 AF XY: 0.451 AC XY: 287034 AN XY: 636190

African (AFR) AF: 0.331 AC: 9595 AN: 29000

American (AMR) AF: 0.470 AC: 13247 AN: 28212

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 11057 AN: 20054

East Asian (EAS) AF: 0.664 AC: 23126 AN: 34838

South Asian (SAS) AF: 0.457 AC: 31052 AN: 67974

European-Finnish (FIN) AF: 0.454 AC: 16055 AN: 35334

Middle Eastern (MID) AF: 0.450 AC: 2074 AN: 4612

European-Non Finnish (NFE) AF: 0.444 AC: 455216 AN: 1026046

Other (OTH) AF: 0.472 AC: 25613 AN: 54240

GnomAD4 genome AF: 0.426 AC: 64852 AN: 152132 Hom.: 14210 Cov.: 34 AF XY: 0.429 AC XY: 31870 AN XY: 74344

African (AFR) AF: 0.333 AC: 13806 AN: 41508

American (AMR) AF: 0.448 AC: 6861 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.542 AC: 1878 AN: 3468

East Asian (EAS) AF: 0.665 AC: 3429 AN: 5158

South Asian (SAS) AF: 0.466 AC: 2252 AN: 4828

European-Finnish (FIN) AF: 0.438 AC: 4635 AN: 10572

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.448 AC: 30476 AN: 67984

Other (OTH) AF: 0.432 AC: 912 AN: 2110

Alfa AF: 0.430 Hom.: 2122

Bravo AF: 0.424

Asia WGS AF: 0.537 AC: 1864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.66
DANN	Benign	0.63
PhyloP100		-0.85
Mutation Taster		=4/96	disease causing

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		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: rs2241511; hg19: chr18-72180723; COSMIC: COSV60841025; COSMIC: COSV60841025;