Genetic Variant CNDP1:c.466+16G>A (chr18-74561034-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_032649.6(CNDP1):c.466+16G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 1,607,108 control chromosomes in the GnomAD database, including 63,401 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 0.23 ( 5049 hom., cov: 31)

Exomes 𝑓: 0.28 ( 58352 hom. )

Consequence

CNDP1
NM_032649.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.17

Publications

9 publications found

Variant links:

Genes affected

CNDP1 (HGNC:20675): (carnosine dipeptidase 1) This gene encodes a member of the M20 metalloprotease family. The encoded protein is specifically expressed in the brain, is a homodimeric dipeptidase which was identified as human carnosinase. This gene contains trinucleotide (CTG) repeat length polymorphism in the coding region. [provided by RefSeq, Jul 2008]

CNDP1 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=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032649.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNDP1	NM_032649.6	MANE Select	c.466+16G>A		intron	N/A	NP_116038.4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CNDP1	ENST00000358821.8	TSL:1 MANE Select	c.466+16G>A	intron	N/A	ENSP00000351682.3
CNDP1	ENST00000582365.1	TSL:5	c.337+16G>A	intron	N/A	ENSP00000462096.1
CNDP1	ENST00000584316.5	TSL:4	n.48+23G>A	intron	N/A	ENSP00000463807.1

Frequencies

GnomAD3 genomes

AF:

0.233

AC:

35376

AN:

151880

Hom.:

5047

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0755

Gnomad AMI

AF:

0.172

Gnomad AMR

AF:

0.353

Gnomad ASJ

AF:

0.201

Gnomad EAS

AF:

0.440

Gnomad SAS

AF:

0.310

Gnomad FIN

AF:

0.336

Gnomad MID

AF:

0.196

Gnomad NFE

AF:

0.267

Gnomad OTH

AF:

0.225

GnomAD2 exomes

AF:

0.299

AC:

74499

AN:

249324

AF XY:

0.297

show subpopulations

Gnomad AFR exome

AF:

0.0744

Gnomad AMR exome

AF:

0.446

Gnomad ASJ exome

AF:

0.194

Gnomad EAS exome

AF:

0.419

Gnomad FIN exome

AF:

0.321

Gnomad NFE exome

AF:

0.267

Gnomad OTH exome

AF:

0.281

GnomAD4 exome

AF:

0.275

AC:

400381

AN:

1455110

Hom.:

58352

Cov.:

AF XY:

0.276

AC XY:

199245

AN XY:

722546

show subpopulations

African (AFR)

AF:

0.0656

AC:

2188

AN:

33362

American (AMR)

AF:

0.434

AC:

19372

AN:

44614

Ashkenazi Jewish (ASJ)

AF:

0.197

AC:

5127

AN:

26088

East Asian (EAS)

AF:

0.495

AC:

19534

AN:

39500

South Asian (SAS)

AF:

0.317

AC:

27272

AN:

86136

European-Finnish (FIN)

AF:

0.320

AC:

16836

AN:

52580

Middle Eastern (MID)

AF:

0.214

AC:

1199

AN:

5608

European-Non Finnish (NFE)

AF:

0.265

AC:

292950

AN:

1107130

Other (OTH)

AF:

0.265

AC:

15903

AN:

60092

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

14919

29839

44758

59678

74597

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10006

20012

30018

40024

50030

<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:

0.233

AC:

35397

AN:

151998

Hom.:

5049

Cov.:

AF XY:

0.239

AC XY:

17782

AN XY:

74282

show subpopulations

African (AFR)

AF:

0.0755

AC:

3133

AN:

41496

American (AMR)

AF:

0.353

AC:

5398

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.201

AC:

699

AN:

3470

East Asian (EAS)

AF:

0.440

AC:

2267

AN:

5148

South Asian (SAS)

AF:

0.310

AC:

1494

AN:

4816

European-Finnish (FIN)

AF:

0.336

AC:

3547

AN:

10550

Middle Eastern (MID)

AF:

0.190

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.267

AC:

18165

AN:

67936

Other (OTH)

AF:

0.229

AC:

482

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1291

2581

3872

5162

6453

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

378

756

1134

1512

1890

<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:

0.239

Hom.:

7787

Bravo

AF:

0.225

Asia WGS

AF:

0.380

AC:

1323

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.21

(source)

DANN

Benign

0.66

PhyloP100

-2.2

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