Genetic Variant CNDP1:c.1168-88C>T (chr18-74580042-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.1168-88C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.678 in 1,164,230 control chromosomes in the GnomAD database, including 269,221 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 0.67 ( 34303 hom., cov: 33)

Exomes 𝑓: 0.68 ( 234918 hom. )

Consequence

CNDP1
NM_032649.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0330

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:

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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=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.777 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNDP1	NM_032649.6 link	c.1168-88C>T		intron_variant	Intron 9 of 11	ENST00000358821.8	NP_116038.4	Q96KN2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
CNDP1	ENST00000358821.8 link	c.1168-88C>T	intron_variant	Intron 9 of 11	1	NM_032649.6	ENSP00000351682.3	Q96KN2
CNDP1	ENST00000582365.1 link	c.1039-88C>T	intron_variant	Intron 8 of 10	5		ENSP00000462096.1	J3KRP0
CNDP1	ENST00000582461.1 link	n.2049-88C>T	intron_variant	Intron 1 of 2	5
CNDP1	ENST00000584004.5 link	n.692-88C>T	intron_variant	Intron 4 of 6	2

Frequencies

GnomAD3 genomes

AF:

0.669

AC:

101608

AN:

151988

Hom.:

34264

Cov.:

show subpopulations

Gnomad AFR

AF:

0.618

Gnomad AMI

AF:

0.651

Gnomad AMR

AF:

0.762

Gnomad ASJ

AF:

0.656

Gnomad EAS

AF:

0.797

Gnomad SAS

AF:

0.759

Gnomad FIN

AF:

0.680

Gnomad MID

AF:

0.709

Gnomad NFE

AF:

0.660

Gnomad OTH

AF:

0.693

GnomAD4 exome

AF:

0.679

AC:

687609

AN:

1012124

Hom.:

234918

AF XY:

0.681

AC XY:

349772

AN XY:

513350

show subpopulations

African (AFR)

AF:

0.613

AC:

14878

AN:

24282

American (AMR)

AF:

0.797

AC:

26528

AN:

33264

Ashkenazi Jewish (ASJ)

AF:

0.645

AC:

13349

AN:

20686

East Asian (EAS)

AF:

0.822

AC:

28923

AN:

35190

South Asian (SAS)

AF:

0.757

AC:

50904

AN:

67288

European-Finnish (FIN)

AF:

0.681

AC:

32603

AN:

47842

Middle Eastern (MID)

AF:

0.714

AC:

3349

AN:

4688

European-Non Finnish (NFE)

AF:

0.663

AC:

486465

AN:

733936

Other (OTH)

AF:

0.681

AC:

30610

AN:

44948

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

10743

21487

32230

42974

53717

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11088

22176

33264

44352

55440

<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:

0.669

AC:

101701

AN:

152106

Hom.:

34303

Cov.:

AF XY:

0.674

AC XY:

50113

AN XY:

74362

show subpopulations

African (AFR)

AF:

0.619

AC:

25659

AN:

41484

American (AMR)

AF:

0.763

AC:

11661

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.656

AC:

2277

AN:

3470

East Asian (EAS)

AF:

0.798

AC:

4115

AN:

5158

South Asian (SAS)

AF:

0.758

AC:

3659

AN:

4826

European-Finnish (FIN)

AF:

0.680

AC:

7195

AN:

10576

Middle Eastern (MID)

AF:

0.701

AC:

206

AN:

294

European-Non Finnish (NFE)

AF:

0.660

AC:

44861

AN:

67984

Other (OTH)

AF:

0.698

AC:

1477

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1763

3525

5288

7050

8813

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

810

1620

2430

3240

4050

<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:

0.654

Hom.:

4075

Bravo

AF:

0.675

Asia WGS

AF:

0.792

AC:

2755

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.70

(source)

DANN

Benign

0.17

PhyloP100

0.033

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