Genetic Variant CNDP2:c.1358+73G>A (chr18-74519169-G-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_018235.3(CNDP2):c.1358+73G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.59 in 1,501,800 control chromosomes in the GnomAD database, including 268,968 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 0.52 ( 22939 hom., cov: 31)

Exomes 𝑓: 0.60 ( 246029 hom. )

Consequence

CNDP2
NM_018235.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.52

Publications

10 publications found

Variant links:

Genes affected

CNDP2 (HGNC:24437): (carnosine dipeptidase 2) CNDP2, also known as tissue carnosinase and peptidase A (EC 3.4.13.18), is a nonspecific dipeptidase rather than a selective carnosinase (Teufel et al., 2003 [PubMed 12473676]).[supplied by OMIM, Mar 2008]

CNDP2 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=-0.99).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018235.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CNDP2	NM_018235.3	MANE Select	c.1358+73G>A	intron	N/A	NP_060705.2
CNDP2	NM_001370248.1		c.1358+73G>A	intron	N/A	NP_001357177.1
CNDP2	NM_001370249.1		c.1358+73G>A	intron	N/A	NP_001357178.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CNDP2	ENST00000324262.9	TSL:1 MANE Select	c.1358+73G>A	intron	N/A	ENSP00000325548.4
CNDP2	ENST00000324301.12	TSL:1	c.1106+73G>A	intron	N/A	ENSP00000325756.8
CNDP2	ENST00000579847.5	TSL:5	c.1358+73G>A	intron	N/A	ENSP00000462311.1

Frequencies

GnomAD3 genomes

AF:

0.523

AC:

79315

AN:

151654

Hom.:

22927

Cov.:

show subpopulations

Gnomad AFR

AF:

0.270

Gnomad AMI

AF:

0.625

Gnomad AMR

AF:

0.680

Gnomad ASJ

AF:

0.613

Gnomad EAS

AF:

0.875

Gnomad SAS

AF:

0.726

Gnomad FIN

AF:

0.560

Gnomad MID

AF:

0.586

Gnomad NFE

AF:

0.588

Gnomad OTH

AF:

0.551

GnomAD4 exome

AF:

0.597

AC:

806274

AN:

1350028

Hom.:

246029

AF XY:

0.600

AC XY:

396092

AN XY:

659820

show subpopulations

African (AFR)

AF:

0.252

AC:

7607

AN:

30238

American (AMR)

AF:

0.774

AC:

23760

AN:

30704

Ashkenazi Jewish (ASJ)

AF:

0.607

AC:

12188

AN:

20076

East Asian (EAS)

AF:

0.886

AC:

33679

AN:

38020

South Asian (SAS)

AF:

0.716

AC:

49924

AN:

69716

European-Finnish (FIN)

AF:

0.577

AC:

27285

AN:

47306

Middle Eastern (MID)

AF:

0.624

AC:

2388

AN:

3826

European-Non Finnish (NFE)

AF:

0.584

AC:

615852

AN:

1054686

Other (OTH)

AF:

0.606

AC:

33591

AN:

55456

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

15275

30549

45824

61098

76373

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

17618

35236

52854

70472

88090

<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:

0.523

AC:

79343

AN:

151772

Hom.:

22939

Cov.:

AF XY:

0.530

AC XY:

39297

AN XY:

74200

show subpopulations

African (AFR)

AF:

0.270

AC:

11159

AN:

41376

American (AMR)

AF:

0.681

AC:

10383

AN:

15252

Ashkenazi Jewish (ASJ)

AF:

0.613

AC:

2126

AN:

3470

East Asian (EAS)

AF:

0.874

AC:

4472

AN:

5114

South Asian (SAS)

AF:

0.727

AC:

3491

AN:

4804

European-Finnish (FIN)

AF:

0.560

AC:

5899

AN:

10540

Middle Eastern (MID)

AF:

0.579

AC:

169

AN:

292

European-Non Finnish (NFE)

AF:

0.588

AC:

39904

AN:

67902

Other (OTH)

AF:

0.555

AC:

1170

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1665

3330

4994

6659

8324

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

694

1388

2082

2776

3470

<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:

0.563

Hom.:

54430

Bravo

AF:

0.520

Asia WGS

AF:

0.784

AC:

2721

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.011

(source)

DANN

Benign

0.51

PhyloP100

-2.5

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