NM_018235.3:c.743-51G>A

Variant names:

• chr18-74513508-G-A
• rs8090744
• NM_018235.3:c.743-51G>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.743-51G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0313 in 1,553,184 control chromosomes in the GnomAD database, including 1,910 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 0.069 (782 hom., cov: 33)
  • Exomes 𝑓: 0.027 (1128 hom.)
• Consequence: CNDP2 NM_018235.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96
• Publications: 3 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018235.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNDP2	NM_018235.3	MANE Select	c.743-51G>A		intron	N/A	NP_060705.2
	CNDP2	NM_001370248.1		c.743-51G>A		intron	N/A	NP_001357177.1
	CNDP2	NM_001370249.1		c.743-51G>A		intron	N/A	NP_001357178.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNDP2	ENST00000324262.9	TSL:1 MANE Select	c.743-51G>A		intron	N/A	ENSP00000325548.4
	CNDP2	ENST00000324301.12	TSL:1	c.491-51G>A		intron	N/A	ENSP00000325756.8
	CNDP2	ENST00000579847.5	TSL:5	c.743-51G>A		intron	N/A	ENSP00000462311.1

Frequencies

GnomAD3 genomes AF: 0.0690 AC: 10498 AN: 152188 Hom.: 780 Cov.: 33

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0325

Gnomad ASJ AF: 0.0533

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0577

Gnomad FIN AF: 0.0128

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0220

Gnomad OTH AF: 0.0549

GnomAD2 exomes AF: 0.0365 AC: 6779 AN: 185968 AF XY: 0.0349

Gnomad AFR exome AF: 0.190

Gnomad AMR exome AF: 0.0177

Gnomad ASJ exome AF: 0.0555

Gnomad EAS exome AF: 0.000633

Gnomad FIN exome AF: 0.0139

Gnomad NFE exome AF: 0.0220

Gnomad OTH exome AF: 0.0325

GnomAD4 exome AF: 0.0272 AC: 38105 AN: 1400878 Hom.: 1128 Cov.: 29 AF XY: 0.0278 AC XY: 19261 AN XY: 691946

African (AFR) AF: 0.192 AC: 6210 AN: 32330

American (AMR) AF: 0.0200 AC: 793 AN: 39576

Ashkenazi Jewish (ASJ) AF: 0.0598 AC: 1364 AN: 22792

East Asian (EAS) AF: 0.000208 AC: 8 AN: 38474

South Asian (SAS) AF: 0.0568 AC: 4415 AN: 77734

European-Finnish (FIN) AF: 0.0149 AC: 634 AN: 42474

Middle Eastern (MID) AF: 0.0494 AC: 265 AN: 5362

European-Non Finnish (NFE) AF: 0.0206 AC: 22345 AN: 1083932

Other (OTH) AF: 0.0356 AC: 2071 AN: 58204

GnomAD4 genome AF: 0.0690 AC: 10512 AN: 152306 Hom.: 782 Cov.: 33 AF XY: 0.0679 AC XY: 5056 AN XY: 74476

African (AFR) AF: 0.188 AC: 7795 AN: 41544

American (AMR) AF: 0.0325 AC: 498 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.0533 AC: 185 AN: 3472

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5174

South Asian (SAS) AF: 0.0577 AC: 279 AN: 4834

European-Finnish (FIN) AF: 0.0128 AC: 136 AN: 10620

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0220 AC: 1495 AN: 68030

Other (OTH) AF: 0.0539 AC: 114 AN: 2116

Alfa AF: 0.0323 Hom.: 97

Bravo AF: 0.0758

Asia WGS AF: 0.0270 AC: 92 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.63
DANN	Benign	0.50
PhyloP100		-2.0
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs8090744; hg19: chr18-72180743;