dbSNP rs8090744: CNDP2:c.743-51G>A (chr18-74513508-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.96

Publications

3 publications found

Variant links:

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]

CNDP2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNDP2	NM_018235.3 link	c.743-51G>A		intron_variant	Intron 7 of 11	ENST00000324262.9	NP_060705.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNDP2	ENST00000324262.9 link	c.743-51G>A		intron_variant	Intron 7 of 11	1	NM_018235.3	ENSP00000325548.4

Frequencies

GnomAD3 genomes

AF:

0.0690

AC:

10498

AN:

152188

Hom.:

780

Cov.:

show subpopulations

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

show subpopulations

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.:

AF XY:

0.0278

AC XY:

19261

AN XY:

691946

show subpopulations

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:

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

1765

3530

5296

7061

8826

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

966

1932

2898

3864

4830

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0690

AC:

10512

AN:

152306

Hom.:

782

Cov.:

AF XY:

0.0679

AC XY:

5056

AN XY:

74476

show subpopulations

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:

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.0220

AC:

1495

AN:

68030

Other (OTH)

AF:

0.0539

AC:

114

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

456

913

1369

1826

2282

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

114

228

342

456

570

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0323

Hom.:

Bravo

AF:

0.0758

Asia WGS

AF:

0.0270

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.63

(source)

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)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over