Genetic Variant CNDP1:c.154-54C>T (chr18-74559269-C-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_032649.6(CNDP1):c.154-54C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 1,596,032 control chromosomes in the GnomAD database, including 98,464 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 0.30 ( 7693 hom., cov: 32)

Exomes 𝑓: 0.35 ( 90771 hom. )

Consequence

CNDP1
NM_032649.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.661

Publications

15 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:

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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=-0.81).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNDP1	NM_032649.6 link	c.154-54C>T		intron_variant	Intron 2 of 11	ENST00000358821.8	NP_116038.4	Q96KN2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
CNDP1	ENST00000358821.8 link	c.154-54C>T	intron_variant	Intron 2 of 11	1	NM_032649.6	ENSP00000351682.3	Q96KN2
CNDP1	ENST00000582365.1 link	c.25-54C>T	intron_variant	Intron 1 of 10	5		ENSP00000462096.1	J3KRP0
CNDP1	ENST00000585136.1 link	n.319-54C>T	intron_variant	Intron 2 of 4	3

Frequencies

GnomAD3 genomes

AF:

0.302

AC:

45912

AN:

152018

Hom.:

7691

Cov.:

show subpopulations

Gnomad AFR

AF:

0.156

Gnomad AMI

AF:

0.363

Gnomad AMR

AF:

0.322

Gnomad ASJ

AF:

0.434

Gnomad EAS

AF:

0.436

Gnomad SAS

AF:

0.384

Gnomad FIN

AF:

0.341

Gnomad MID

AF:

0.389

Gnomad NFE

AF:

0.355

Gnomad OTH

AF:

0.349

GnomAD4 exome

AF:

0.351

AC:

506640

AN:

1443896

Hom.:

90771

AF XY:

0.353

AC XY:

254264

AN XY:

719354

show subpopulations

African (AFR)

AF:

0.148

AC:

4908

AN:

33136

American (AMR)

AF:

0.337

AC:

14991

AN:

44456

Ashkenazi Jewish (ASJ)

AF:

0.439

AC:

11382

AN:

25956

East Asian (EAS)

AF:

0.391

AC:

15498

AN:

39592

South Asian (SAS)

AF:

0.388

AC:

33322

AN:

85790

European-Finnish (FIN)

AF:

0.351

AC:

18581

AN:

52932

Middle Eastern (MID)

AF:

0.425

AC:

2395

AN:

5630

European-Non Finnish (NFE)

AF:

0.350

AC:

384295

AN:

1096612

Other (OTH)

AF:

0.356

AC:

21268

AN:

59792

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

16833

33666

50498

67331

84164

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

12142

24284

36426

48568

60710

<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:

0.302

AC:

45933

AN:

152136

Hom.:

7693

Cov.:

AF XY:

0.306

AC XY:

22727

AN XY:

74346

show subpopulations

African (AFR)

AF:

0.156

AC:

6487

AN:

41532

American (AMR)

AF:

0.323

AC:

4934

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.434

AC:

1506

AN:

3468

East Asian (EAS)

AF:

0.436

AC:

2252

AN:

5168

South Asian (SAS)

AF:

0.385

AC:

1855

AN:

4820

European-Finnish (FIN)

AF:

0.341

AC:

3604

AN:

10570

Middle Eastern (MID)

AF:

0.387

AC:

113

AN:

292

European-Non Finnish (NFE)

AF:

0.355

AC:

24108

AN:

67974

Other (OTH)

AF:

0.352

AC:

743

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1608

3217

4825

6434

8042

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

472

944

1416

1888

2360

<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:

0.350

Hom.:

15589

Bravo

AF:

0.295

Asia WGS

AF:

0.395

AC:

1370

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

0.47

(source)

DANN

Benign

0.57

PhyloP100

-0.66

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