Genetic Variant NM_032649.6:c.174C>A (chr18-74559343-C-A) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_032649.6(CNDP1):c.174C>A(p.Ala58Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0321 in 1,613,966 control chromosomes in the GnomAD database, including 1,441 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 0.058 ( 474 hom., cov: 32)

Exomes 𝑓: 0.029 ( 967 hom. )

Consequence

CNDP1
NM_032649.6 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.71

Publications

8 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 -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.6).

BP7

Synonymous conserved (PhyloP=-4.71 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNDP1	NM_032649.6 link	c.174C>A	p.Ala58Ala	synonymous_variant	Exon 3 of 12	ENST00000358821.8	NP_116038.4	Q96KN2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
CNDP1	ENST00000358821.8 link	c.174C>A	p.Ala58Ala	synonymous_variant	Exon 3 of 12	1	NM_032649.6	ENSP00000351682.3	Q96KN2
CNDP1	ENST00000582365.1 link	c.45C>A	p.Ala15Ala	synonymous_variant	Exon 2 of 11	5		ENSP00000462096.1	J3KRP0
CNDP1	ENST00000585136.1 link	n.339C>A		non_coding_transcript_exon_variant	Exon 3 of 5	3

Frequencies

GnomAD3 genomes

AF:

0.0584

AC:

8885

AN:

152086

Hom.:

472

Cov.:

show subpopulations

Gnomad AFR

AF:

0.137

Gnomad AMI

AF:

0.00987

Gnomad AMR

AF:

0.0344

Gnomad ASJ

AF:

0.0167

Gnomad EAS

AF:

0.0661

Gnomad SAS

AF:

0.0257

Gnomad FIN

AF:

0.0200

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.0267

Gnomad OTH

AF:

0.0556

GnomAD2 exomes

AF:

0.0346

AC:

8691

AN:

251306

AF XY:

0.0324

show subpopulations

Gnomad AFR exome

AF:

0.144

Gnomad AMR exome

AF:

0.0183

Gnomad ASJ exome

AF:

0.0192

Gnomad EAS exome

AF:

0.0640

Gnomad FIN exome

AF:

0.0240

Gnomad NFE exome

AF:

0.0262

Gnomad OTH exome

AF:

0.0302

GnomAD4 exome

AF:

0.0294

AC:

42959

AN:

1461762

Hom.:

967

Cov.:

AF XY:

0.0290

AC XY:

21058

AN XY:

727184

show subpopulations

African (AFR)

AF:

0.148

AC:

4953

AN:

33470

American (AMR)

AF:

0.0205

AC:

915

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.0191

AC:

499

AN:

26132

East Asian (EAS)

AF:

0.0596

AC:

2366

AN:

39694

South Asian (SAS)

AF:

0.0230

AC:

1981

AN:

86252

European-Finnish (FIN)

AF:

0.0256

AC:

1364

AN:

53366

Middle Eastern (MID)

AF:

0.0345

AC:

199

AN:

5764

European-Non Finnish (NFE)

AF:

0.0256

AC:

28505

AN:

1111970

Other (OTH)

AF:

0.0360

AC:

2177

AN:

60392

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.480

Heterozygous variant carriers

2100

4199

6299

8398

10498

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1126

2252

3378

4504

5630

<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:

0.0584

AC:

8895

AN:

152204

Hom.:

474

Cov.:

AF XY:

0.0578

AC XY:

4300

AN XY:

74410

show subpopulations

African (AFR)

AF:

0.137

AC:

5681

AN:

41496

American (AMR)

AF:

0.0343

AC:

525

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.0167

AC:

AN:

3470

East Asian (EAS)

AF:

0.0657

AC:

340

AN:

5176

South Asian (SAS)

AF:

0.0257

AC:

124

AN:

4824

European-Finnish (FIN)

AF:

0.0200

AC:

212

AN:

10622

Middle Eastern (MID)

AF:

0.0578

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0267

AC:

1813

AN:

68016

Other (OTH)

AF:

0.0550

AC:

116

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

405

810

1215

1620

2025

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

192

288

384

480

<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:

0.0382

Hom.:

351

Bravo

AF:

0.0645

Asia WGS

AF:

0.0450

AC:

156

AN:

3478

EpiCase

AF:

0.0267

EpiControl

AF:

0.0235

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.60

CADD

Benign

1.7

(source)

DANN

Benign

0.80

PhyloP100

-4.7

Mutation Taster

=98/2

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