rs2241508

chr18-74519169-G-Achr18-74519169-G-C

Variant summary

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

The NM_018235.3(CNDP2):c.1358+73G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.59 in 1,501,800 control chromosomes in the GnomAD database, including 268,968 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 0.52 (22939 hom., cov: 31)
  • Exomes 𝑓: 0.60 (246029 hom.)
• Consequence: CNDP2 NM_018235.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.52

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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CNDP2	NM_018235.3	c.1358+73G>A		intron_variant		ENST00000324262.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CNDP2	ENST00000324262.9	c.1358+73G>A		intron_variant		1	NM_018235.3	P1

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79315 AN: 151654 Hom.: 22927 Cov.: 31

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.625

Gnomad AMR AF: 0.680

Gnomad ASJ AF: 0.613

Gnomad EAS AF: 0.875

Gnomad SAS AF: 0.726

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.551

GnomAD4 exome AF: 0.597 AC: 806274 AN: 1350028 Hom.: 246029 AF XY: 0.600 AC XY: 396092 AN XY: 659820

Gnomad4 AFR exome AF: 0.252

Gnomad4 AMR exome AF: 0.774

Gnomad4 ASJ exome AF: 0.607

Gnomad4 EAS exome AF: 0.886

Gnomad4 SAS exome AF: 0.716

Gnomad4 FIN exome AF: 0.577

Gnomad4 NFE exome AF: 0.584

Gnomad4 OTH exome AF: 0.606

GnomAD4 genome AF: 0.523 AC: 79343 AN: 151772 Hom.: 22939 Cov.: 31 AF XY: 0.530 AC XY: 39297 AN XY: 74200

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.681

Gnomad4 ASJ AF: 0.613

Gnomad4 EAS AF: 0.874

Gnomad4 SAS AF: 0.727

Gnomad4 FIN AF: 0.560

Gnomad4 NFE AF: 0.588

Gnomad4 OTH AF: 0.555

Alfa AF: 0.586 Hom.: 37195

Bravo AF: 0.520

Asia WGS AF: 0.784 AC: 2721 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.011
Dann	Benign	0.51

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: rs2241508; hg19: chr18-72186404; COSMIC: COSV60841976; COSMIC: COSV60841976;