Genetic Variant CNDP2:p.Tyr190Tyr (chr18-74510926-T-C) – 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.570T>C(p.Tyr190Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 1,613,812 control chromosomes in the GnomAD database, including 33,025 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 0.18 ( 2650 hom., cov: 32)

Exomes 𝑓: 0.20 ( 30375 hom. )

Consequence

CNDP2
NM_018235.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.343

Publications

35 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=-0.66).

BP7

Synonymous conserved (PhyloP=-0.343 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNDP2	NM_018235.3 link	c.570T>C	p.Tyr190Tyr	synonymous_variant	Exon 6 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.570T>C	p.Tyr190Tyr	synonymous_variant	Exon 6 of 12	1	NM_018235.3	ENSP00000325548.4		Q96KP4-1

Frequencies

GnomAD3 genomes

AF:

0.176

AC:

26712

AN:

152096

Hom.:

2642

Cov.:

show subpopulations

Gnomad AFR

AF:

0.108

Gnomad AMI

AF:

0.144

Gnomad AMR

AF:

0.279

Gnomad ASJ

AF:

0.155

Gnomad EAS

AF:

0.288

Gnomad SAS

AF:

0.237

Gnomad FIN

AF:

0.114

Gnomad MID

AF:

0.190

Gnomad NFE

AF:

0.191

Gnomad OTH

AF:

0.186

GnomAD2 exomes

AF:

0.209

AC:

52581

AN:

251452

AF XY:

0.208

show subpopulations

Gnomad AFR exome

AF:

0.109

Gnomad AMR exome

AF:

0.338

Gnomad ASJ exome

AF:

0.150

Gnomad EAS exome

AF:

0.297

Gnomad FIN exome

AF:

0.115

Gnomad NFE exome

AF:

0.188

Gnomad OTH exome

AF:

0.197

GnomAD4 exome

AF:

0.199

AC:

290947

AN:

1461598

Hom.:

30375

Cov.:

AF XY:

0.200

AC XY:

145286

AN XY:

727120

show subpopulations

African (AFR)

AF:

0.107

AC:

3588

AN:

33476

American (AMR)

AF:

0.334

AC:

14953

AN:

44720

Ashkenazi Jewish (ASJ)

AF:

0.148

AC:

3862

AN:

26134

East Asian (EAS)

AF:

0.296

AC:

11741

AN:

39700

South Asian (SAS)

AF:

0.232

AC:

20035

AN:

86248

European-Finnish (FIN)

AF:

0.119

AC:

6355

AN:

53420

Middle Eastern (MID)

AF:

0.189

AC:

1089

AN:

5762

European-Non Finnish (NFE)

AF:

0.196

AC:

218102

AN:

1111754

Other (OTH)

AF:

0.186

AC:

11222

AN:

60384

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.470

Heterozygous variant carriers

12436

24871

37307

49742

62178

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7860

15720

23580

31440

39300

<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:

0.176

AC:

26724

AN:

152214

Hom.:

2650

Cov.:

AF XY:

0.177

AC XY:

13197

AN XY:

74422

show subpopulations

African (AFR)

AF:

0.108

AC:

4497

AN:

41532

American (AMR)

AF:

0.280

AC:

4282

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.155

AC:

537

AN:

3468

East Asian (EAS)

AF:

0.288

AC:

1487

AN:

5164

South Asian (SAS)

AF:

0.236

AC:

1137

AN:

4828

European-Finnish (FIN)

AF:

0.114

AC:

1213

AN:

10606

Middle Eastern (MID)

AF:

0.187

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.191

AC:

12994

AN:

68004

Other (OTH)

AF:

0.185

AC:

391

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1098

2195

3293

4390

5488

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

292

584

876

1168

1460

<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:

0.183

Hom.:

4508

Bravo

AF:

0.184

Asia WGS

AF:

0.270

AC:

942

AN:

3478

EpiCase

AF:

0.189

EpiControl

AF:

0.185

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

1.5

(source)

DANN

Benign

0.29

PhyloP100

-0.34

PromoterAI

0.049

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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