dbSNP rs7239132: CNDP1:c.303+102C>A (chr18-74559574-C-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.303+102C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 1,061,876 control chromosomes in the GnomAD database, including 75,646 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 0.39 ( 11738 hom., cov: 31)

Exomes 𝑓: 0.37 ( 63908 hom. )

Consequence

CNDP1
NM_032649.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0520

Publications

5 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=-0.91).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNDP1	NM_032649.6 link	c.303+102C>A		intron_variant	Intron 3 of 11	ENST00000358821.8	NP_116038.4	Q96KN2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
CNDP1	ENST00000358821.8 link	c.303+102C>A	intron_variant	Intron 3 of 11	1	NM_032649.6	ENSP00000351682.3	Q96KN2
CNDP1	ENST00000582365.1 link	c.174+102C>A	intron_variant	Intron 2 of 10	5		ENSP00000462096.1	J3KRP0
CNDP1	ENST00000585136.1 link	n.468+102C>A	intron_variant	Intron 3 of 4	3

Frequencies

GnomAD3 genomes

AF:

0.391

AC:

59313

AN:

151826

Hom.:

11727

Cov.:

show subpopulations

Gnomad AFR

AF:

0.412

Gnomad AMI

AF:

0.427

Gnomad AMR

AF:

0.444

Gnomad ASJ

AF:

0.350

Gnomad EAS

AF:

0.373

Gnomad SAS

AF:

0.314

Gnomad FIN

AF:

0.455

Gnomad MID

AF:

0.282

Gnomad NFE

AF:

0.365

Gnomad OTH

AF:

0.356

GnomAD4 exome

AF:

0.369

AC:

335448

AN:

909934

Hom.:

63908

AF XY:

0.366

AC XY:

167226

AN XY:

457192

show subpopulations

African (AFR)

AF:

0.409

AC:

8471

AN:

20700

American (AMR)

AF:

0.465

AC:

8747

AN:

18812

Ashkenazi Jewish (ASJ)

AF:

0.334

AC:

5832

AN:

17450

East Asian (EAS)

AF:

0.455

AC:

14774

AN:

32470

South Asian (SAS)

AF:

0.307

AC:

17222

AN:

56090

European-Finnish (FIN)

AF:

0.437

AC:

14144

AN:

32354

Middle Eastern (MID)

AF:

0.274

AC:

818

AN:

2982

European-Non Finnish (NFE)

AF:

0.364

AC:

250551

AN:

687832

Other (OTH)

AF:

0.361

AC:

14889

AN:

41244

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

10248

20496

30745

40993

51241

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7020

14040

21060

28080

35100

<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:

0.391

AC:

59355

AN:

151942

Hom.:

11738

Cov.:

AF XY:

0.391

AC XY:

29025

AN XY:

74250

show subpopulations

African (AFR)

AF:

0.412

AC:

17084

AN:

41450

American (AMR)

AF:

0.444

AC:

6783

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.350

AC:

1214

AN:

3466

East Asian (EAS)

AF:

0.374

AC:

1922

AN:

5142

South Asian (SAS)

AF:

0.313

AC:

1509

AN:

4816

European-Finnish (FIN)

AF:

0.455

AC:

4798

AN:

10546

Middle Eastern (MID)

AF:

0.289

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.365

AC:

24818

AN:

67932

Other (OTH)

AF:

0.357

AC:

755

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1852

3704

5555

7407

9259

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

564

1128

1692

2256

2820

<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:

0.369

Hom.:

7091

Bravo

AF:

0.391

Asia WGS

AF:

0.377

AC:

1312

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.35

(source)

DANN

Benign

0.70

PhyloP100

-0.052

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