Genetic Variant CNDP1:c.467-115C>G (chr18-74561932-C-G) – 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.467-115C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 793,004 control chromosomes in the GnomAD database, including 21,448 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 0.24 ( 4618 hom., cov: 33)

Exomes 𝑓: 0.22 ( 16830 hom. )

Consequence

CNDP1
NM_032649.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.333

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:

ENSG00000264340 (HGNC:58557):

ENSG00000264340 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 (AFR) allele frequency at 95% confidence interval = 0.308 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNDP1	NM_032649.6	MANE Select	c.467-115C>G		intron	N/A	NP_116038.4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CNDP1	ENST00000358821.8	TSL:1 MANE Select	c.467-115C>G	intron	N/A	ENSP00000351682.3	Q96KN2
CNDP1	ENST00000864762.1		c.467-115C>G	intron	N/A	ENSP00000534821.1
CNDP1	ENST00000954332.1		c.467-115C>G	intron	N/A	ENSP00000624391.1

Frequencies

GnomAD3 genomes

AF:

0.238

AC:

36147

AN:

152014

Hom.:

4612

Cov.:

show subpopulations

Gnomad AFR

AF:

0.313

Gnomad AMI

AF:

0.150

Gnomad AMR

AF:

0.173

Gnomad ASJ

AF:

0.228

Gnomad EAS

AF:

0.0678

Gnomad SAS

AF:

0.285

Gnomad FIN

AF:

0.170

Gnomad MID

AF:

0.285

Gnomad NFE

AF:

0.228

Gnomad OTH

AF:

0.230

GnomAD4 exome

AF:

0.222

AC:

142233

AN:

640870

Hom.:

16830

AF XY:

0.224

AC XY:

75516

AN XY:

336628

show subpopulations

African (AFR)

AF:

0.320

AC:

5455

AN:

17052

American (AMR)

AF:

0.137

AC:

4054

AN:

29574

Ashkenazi Jewish (ASJ)

AF:

0.233

AC:

4178

AN:

17902

East Asian (EAS)

AF:

0.0620

AC:

2043

AN:

32960

South Asian (SAS)

AF:

0.270

AC:

16335

AN:

60432

European-Finnish (FIN)

AF:

0.177

AC:

7244

AN:

40816

Middle Eastern (MID)

AF:

0.266

AC:

1068

AN:

4010

European-Non Finnish (NFE)

AF:

0.233

AC:

94428

AN:

405880

Other (OTH)

AF:

0.230

AC:

7428

AN:

32244

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

5315

10631

15946

21262

26577

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1678

3356

5034

6712

8390

<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:

0.238

AC:

36156

AN:

152134

Hom.:

4618

Cov.:

AF XY:

0.233

AC XY:

17315

AN XY:

74382

show subpopulations

African (AFR)

AF:

0.313

AC:

12977

AN:

41474

American (AMR)

AF:

0.173

AC:

2640

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.228

AC:

791

AN:

3472

East Asian (EAS)

AF:

0.0673

AC:

349

AN:

5182

South Asian (SAS)

AF:

0.284

AC:

1369

AN:

4822

European-Finnish (FIN)

AF:

0.170

AC:

1799

AN:

10586

Middle Eastern (MID)

AF:

0.293

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.228

AC:

15527

AN:

68002

Other (OTH)

AF:

0.227

AC:

481

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1439

2877

4316

5754

7193

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

382

764

1146

1528

1910

<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:

0.229

Hom.:

500

Bravo

AF:

0.240

Asia WGS

AF:

0.158

AC:

551

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.7

(source)

DANN

Benign

0.54

PhyloP100

0.33

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