dbSNP rs2303463: CNDP2:p.Pro35Pro (chr18-74501373-G-A) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_018235.3(CNDP2):c.105G>A(p.Pro35Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 1,613,618 control chromosomes in the GnomAD database, including 34,642 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 0.21 ( 3456 hom., cov: 32)

Exomes 𝑓: 0.20 ( 31186 hom. )

Consequence

CNDP2
NM_018235.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -8.34

Publications

36 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 -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.73).

BP7

Synonymous conserved (PhyloP=-8.34 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNDP2	NM_018235.3 link	c.105G>A	p.Pro35Pro	synonymous_variant	Exon 3 of 12	ENST00000324262.9	NP_060705.2	Q96KP4-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNDP2	ENST00000324262.9 link	c.105G>A	p.Pro35Pro	synonymous_variant	Exon 3 of 12	1	NM_018235.3	ENSP00000325548.4		Q96KP4-1

Frequencies

GnomAD3 genomes

AF:

0.208

AC:

31622

AN:

151960

Hom.:

3444

Cov.:

show subpopulations

Gnomad AFR

AF:

0.222

Gnomad AMI

AF:

0.132

Gnomad AMR

AF:

0.291

Gnomad ASJ

AF:

0.148

Gnomad EAS

AF:

0.286

Gnomad SAS

AF:

0.250

Gnomad FIN

AF:

0.116

Gnomad MID

AF:

0.196

Gnomad NFE

AF:

0.191

Gnomad OTH

AF:

0.214

GnomAD2 exomes

AF:

0.218

AC:

54743

AN:

251172

AF XY:

0.216

show subpopulations

Gnomad AFR exome

AF:

0.226

Gnomad AMR exome

AF:

0.342

Gnomad ASJ exome

AF:

0.145

Gnomad EAS exome

AF:

0.293

Gnomad FIN exome

AF:

0.115

Gnomad NFE exome

AF:

0.187

Gnomad OTH exome

AF:

0.200

GnomAD4 exome

AF:

0.202

AC:

294983

AN:

1461538

Hom.:

31186

Cov.:

AF XY:

0.203

AC XY:

147341

AN XY:

727088

show subpopulations

African (AFR)

AF:

0.225

AC:

7515

AN:

33470

American (AMR)

AF:

0.339

AC:

15151

AN:

44662

Ashkenazi Jewish (ASJ)

AF:

0.143

AC:

3724

AN:

26122

East Asian (EAS)

AF:

0.293

AC:

11625

AN:

39666

South Asian (SAS)

AF:

0.246

AC:

21208

AN:

86206

European-Finnish (FIN)

AF:

0.119

AC:

6373

AN:

53416

Middle Eastern (MID)

AF:

0.204

AC:

1176

AN:

5756

European-Non Finnish (NFE)

AF:

0.195

AC:

216582

AN:

1111868

Other (OTH)

AF:

0.193

AC:

11629

AN:

60372

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.477

Heterozygous variant carriers

12572

25144

37715

50287

62859

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7866

15732

23598

31464

39330

<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:

0.208

AC:

31655

AN:

152080

Hom.:

3456

Cov.:

AF XY:

0.210

AC XY:

15603

AN XY:

74350

show subpopulations

African (AFR)

AF:

0.222

AC:

9189

AN:

41474

American (AMR)

AF:

0.292

AC:

4457

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.148

AC:

513

AN:

3470

East Asian (EAS)

AF:

0.286

AC:

1477

AN:

5162

South Asian (SAS)

AF:

0.249

AC:

1199

AN:

4820

European-Finnish (FIN)

AF:

0.116

AC:

1230

AN:

10578

Middle Eastern (MID)

AF:

0.197

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.191

AC:

12959

AN:

67980

Other (OTH)

AF:

0.214

AC:

453

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1289

2579

3868

5158

6447

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

334

668

1002

1336

1670

<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:

0.200

Hom.:

9611

Bravo

AF:

0.220

Asia WGS

AF:

0.288

AC:

1004

AN:

3478

EpiCase

AF:

0.188

EpiControl

AF:

0.184

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.21

BayesDel_noAF

Benign

-0.73

CADD

Benign

1.2

(source)

DANN

Benign

0.82

PhyloP100

-8.3

PromoterAI

-0.021

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Mutation Taster

=97/3

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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