Genetic Variant NM_032649.6:c.556-131A>C (chr18-74567102-A-C) – 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.556-131A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 694,244 control chromosomes in the GnomAD database, including 132,748 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 0.56 ( 25158 hom., cov: 31)

Exomes 𝑓: 0.62 ( 107590 hom. )

Consequence

CNDP1
NM_032649.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.02

Publications

3 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=-1.08).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.664 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.556-131A>C		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.556-131A>C	intron	N/A	ENSP00000351682.3	Q96KN2
CNDP1	ENST00000864762.1		c.556-131A>C	intron	N/A	ENSP00000534821.1
CNDP1	ENST00000954332.1		c.556-131A>C	intron	N/A	ENSP00000624391.1

Frequencies

GnomAD3 genomes

AF:

0.560

AC:

85030

AN:

151904

Hom.:

25152

Cov.:

show subpopulations

Gnomad AFR

AF:

0.363

Gnomad AMI

AF:

0.738

Gnomad AMR

AF:

0.569

Gnomad ASJ

AF:

0.627

Gnomad EAS

AF:

0.410

Gnomad SAS

AF:

0.529

Gnomad FIN

AF:

0.657

Gnomad MID

AF:

0.570

Gnomad NFE

AF:

0.669

Gnomad OTH

AF:

0.590

GnomAD4 exome

AF:

0.622

AC:

337219

AN:

542222

Hom.:

107590

AF XY:

0.619

AC XY:

179004

AN XY:

289094

show subpopulations

African (AFR)

AF:

0.357

AC:

5180

AN:

14498

American (AMR)

AF:

0.576

AC:

16407

AN:

28468

Ashkenazi Jewish (ASJ)

AF:

0.639

AC:

10409

AN:

16300

East Asian (EAS)

AF:

0.363

AC:

11591

AN:

31898

South Asian (SAS)

AF:

0.539

AC:

28450

AN:

52812

European-Finnish (FIN)

AF:

0.667

AC:

28040

AN:

42064

Middle Eastern (MID)

AF:

0.623

AC:

1762

AN:

2828

European-Non Finnish (NFE)

AF:

0.671

AC:

217444

AN:

324050

Other (OTH)

AF:

0.612

AC:

17936

AN:

29304

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

6658

13315

19973

26630

33288

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1456

2912

4368

5824

7280

<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:

0.559

AC:

85051

AN:

152022

Hom.:

25158

Cov.:

AF XY:

0.557

AC XY:

41399

AN XY:

74330

show subpopulations

African (AFR)

AF:

0.362

AC:

15011

AN:

41434

American (AMR)

AF:

0.569

AC:

8699

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.627

AC:

2175

AN:

3468

East Asian (EAS)

AF:

0.409

AC:

2113

AN:

5160

South Asian (SAS)

AF:

0.529

AC:

2547

AN:

4812

European-Finnish (FIN)

AF:

0.657

AC:

6946

AN:

10574

Middle Eastern (MID)

AF:

0.565

AC:

166

AN:

294

European-Non Finnish (NFE)

AF:

0.669

AC:

45476

AN:

67968

Other (OTH)

AF:

0.589

AC:

1246

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1791

3582

5374

7165

8956

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

722

1444

2166

2888

3610

<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:

0.486

Hom.:

1577

Bravo

AF:

0.546

Asia WGS

AF:

0.460

AC:

1598

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

0.034

(source)

DANN

Benign

0.11

PhyloP100

-3.0

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