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.

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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CNDP2	NM_018235.3	MANE Select	c.743-51G>A	intron	N/A	NP_060705.2	Q96KP4-1
CNDP2	NM_001370248.1		c.743-51G>A	intron	N/A	NP_001357177.1	Q96KP4-1
CNDP2	NM_001370249.1		c.743-51G>A	intron	N/A	NP_001357178.1	Q96KP4-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CNDP2	ENST00000324262.9	TSL:1 MANE Select	c.743-51G>A	intron	N/A	ENSP00000325548.4	Q96KP4-1
CNDP2	ENST00000324301.12	TSL:1	c.491-51G>A	intron	N/A	ENSP00000325756.8	Q96KP4-2
CNDP2	ENST00000880651.1		c.860-51G>A	intron	N/A	ENSP00000550710.1

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over