Genetic Variant CNDP2:c.657+52G>T (chr18-74511065-G-T) – 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.657+52G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 1,501,194 control chromosomes in the GnomAD database, including 29,718 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 ( 2652 hom., cov: 32)

Exomes 𝑓: 0.20 ( 27066 hom. )

Consequence

CNDP2
NM_018235.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.256

Publications

14 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:

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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=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.276 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
CNDP2	NM_018235.3	MANE Select	c.657+52G>T	intron	N/A	NP_060705.2
CNDP2	NM_001370254.1		c.-229G>T	5_prime_UTR	Exon 6 of 12	NP_001357183.1
CNDP2	NM_001370248.1		c.657+52G>T	intron	N/A	NP_001357177.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CNDP2	ENST00000324262.9	TSL:1 MANE Select	c.657+52G>T	intron	N/A	ENSP00000325548.4
CNDP2	ENST00000324301.12	TSL:1	c.405+52G>T	intron	N/A	ENSP00000325756.8
CNDP2	ENST00000577669.5	TSL:3	n.79G>T	non_coding_transcript_exon	Exon 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.176

AC:

26711

AN:

151960

Hom.:

2644

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:

0.238

Gnomad FIN

AF:

0.115

Gnomad MID

AF:

0.191

Gnomad NFE

AF:

0.191

Gnomad OTH

AF:

0.186

GnomAD2 exomes

AF:

0.205

AC:

41036

AN:

200454

AF XY:

0.204

show subpopulations

Gnomad AFR exome

AF:

0.110

Gnomad AMR exome

AF:

0.327

Gnomad ASJ exome

AF:

0.145

Gnomad EAS exome

AF:

0.294

Gnomad FIN exome

AF:

0.113

Gnomad NFE exome

AF:

0.185

Gnomad OTH exome

AF:

0.190

GnomAD4 exome

AF:

0.196

AC:

264045

AN:

1349116

Hom.:

27066

Cov.:

AF XY:

0.197

AC XY:

131829

AN XY:

670706

show subpopulations

African (AFR)

AF:

0.106

AC:

3265

AN:

30872

American (AMR)

AF:

0.324

AC:

12175

AN:

37522

Ashkenazi Jewish (ASJ)

AF:

0.144

AC:

3338

AN:

23246

East Asian (EAS)

AF:

0.294

AC:

11407

AN:

38788

South Asian (SAS)

AF:

0.228

AC:

17730

AN:

77670

European-Finnish (FIN)

AF:

0.119

AC:

6024

AN:

50830

Middle Eastern (MID)

AF:

0.175

AC:

780

AN:

4456

European-Non Finnish (NFE)

AF:

0.193

AC:

199014

AN:

1029526

Other (OTH)

AF:

0.183

AC:

10312

AN:

56206

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

Heterozygous variant carriers

9703

19406

29109

38812

48515

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7116

14232

21348

28464

35580

<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:

26723

AN:

152078

Hom.:

2652

Cov.:

AF XY:

0.178

AC XY:

13201

AN XY:

74362

show subpopulations

African (AFR)

AF:

0.108

AC:

4487

AN:

41484

American (AMR)

AF:

0.280

AC:

4274

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.155

AC:

539

AN:

3470

East Asian (EAS)

AF:

0.289

AC:

1491

AN:

5168

South Asian (SAS)

AF:

0.236

AC:

1139

AN:

4824

European-Finnish (FIN)

AF:

0.115

AC:

1213

AN:

10584

Middle Eastern (MID)

AF:

0.188

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.191

AC:

13004

AN:

67966

Other (OTH)

AF:

0.185

AC:

390

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1102

2204

3307

4409

5511

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:

0.153

Hom.:

762

Bravo

AF:

0.184

Asia WGS

AF:

0.270

AC:

943

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

(source)

DANN

Benign

0.77

PhyloP100

-0.26

PromoterAI

0.013

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.14

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