rs12964619

Positions:

• chr18-74496175-G-A
• chr18-74496175-G-C

Variant summary

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

The ENST00000581272.5(CNDP2):​c.-38+252G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 152,350 control chromosomes in the GnomAD database, including 4,815 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 0.24 (4809 hom., cov: 34)
  • Exomes 𝑓: 0.28 (6 hom.)
• Consequence: CNDP2 ENST00000581272.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.165

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=-1.06).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CNDP2	ENST00000581272.5	c.-38+252G>A		intron_variant		4		ENSP00000464151

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36943 AN: 152080 Hom.: 4802 Cov.: 34

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.258

GnomAD4 exome AF: 0.283 AC: 43 AN: 152 Hom.: 6 Cov.: 0 AF XY: 0.281 AC XY: 32 AN XY: 114

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.500

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.125

Gnomad4 NFE exome AF: 0.276

Gnomad4 OTH exome AF: 0.350

GnomAD4 genome AF: 0.243 AC: 36964 AN: 152198 Hom.: 4809 Cov.: 34 AF XY: 0.244 AC XY: 18189 AN XY: 74424

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.209

Gnomad4 EAS AF: 0.297

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.274

Gnomad4 OTH AF: 0.259

Alfa AF: 0.269 Hom.: 1761

Bravo AF: 0.242

Asia WGS AF: 0.324 AC: 1130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	6.4
DANN	Benign	0.87

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs12964619; hg19: chr18-72163410;