rs12971120

Variant names:

• chr18-74506788-A-G
• rs12971120
• NM_018235.3:c.367+777A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 25 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=-0.9).
• 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 rank	MANE	Protein	UniProt
CNDP2	NM_018235.3	c.367+777A>G		intron_variant	Intron 4 of 11	ENST00000324262.9	NP_060705.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNDP2	ENST00000324262.9	c.367+777A>G		intron_variant	Intron 4 of 11	1	NM_018235.3	ENSP00000325548.4

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

African (AFR) AF: 0.120 AC: 4990 AN: 41504

American (AMR) AF: 0.295 AC: 4508 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 586 AN: 3472

East Asian (EAS) AF: 0.295 AC: 1521 AN: 5164

South Asian (SAS) AF: 0.260 AC: 1254 AN: 4828

European-Finnish (FIN) AF: 0.134 AC: 1420 AN: 10612

Middle Eastern (MID) AF: 0.202 AC: 59 AN: 292

European-Non Finnish (NFE) AF: 0.225 AC: 15273 AN: 68002

Other (OTH) AF: 0.211 AC: 445 AN: 2114

Alfa AF: 0.217 Hom.: 6014

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
PhyloP100		-2.6
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12971120; hg19: chr18-72174023;