rs12971120

Positions:

• chr18-74506788-A-G

Variant summary

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

The NM_018235.3(CNDP2):​c.367+777A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 152,188 control chromosomes in the GnomAD database, including 3,319 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 0.20 (3319 hom., cov: 33)
• Consequence: CNDP2 NM_018235.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.65

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CNDP2	NM_018235.3	c.367+777A>G		intron_variant		ENST00000324262.9	NP_060705.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CNDP2	ENST00000324262.9	c.367+777A>G		intron_variant		1	NM_018235.3	ENSP00000325548	P1

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30283 AN: 152070 Hom.: 3308 Cov.: 33

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.212

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.199 AC: 30304 AN: 152188 Hom.: 3319 Cov.: 33 AF XY: 0.200 AC XY: 14887 AN XY: 74416

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.169

Gnomad4 EAS AF: 0.295

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.211

Alfa AF: 0.205 Hom.: 419

Bravo AF: 0.206

Asia WGS AF: 0.289 AC: 1006 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.33
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: rs12971120; hg19: chr18-72174023;