Genetic Variant CNDP2:c.1210+97G>A (chr18-74518737-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.1210+97G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.965 in 1,528,196 control chromosomes in the GnomAD database, including 714,188 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 0.91 ( 64107 hom., cov: 33)

Exomes 𝑓: 0.97 ( 650081 hom. )

Consequence

CNDP2
NM_018235.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.01

Publications

4 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=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.976 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.1210+97G>A	intron	N/A	NP_060705.2
CNDP2	NM_001370248.1		c.1210+97G>A	intron	N/A	NP_001357177.1
CNDP2	NM_001370249.1		c.1210+97G>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.1210+97G>A	intron	N/A	ENSP00000325548.4
CNDP2	ENST00000324301.12	TSL:1	c.958+97G>A	intron	N/A	ENSP00000325756.8
CNDP2	ENST00000577409.1	TSL:2	n.301G>A	non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.912

AC:

138772

AN:

152098

Hom.:

64098

Cov.:

show subpopulations

Gnomad AFR

AF:

0.754

Gnomad AMI

AF:

0.923

Gnomad AMR

AF:

0.945

Gnomad ASJ

AF:

0.997

Gnomad EAS

AF:

0.887

Gnomad SAS

AF:

0.951

Gnomad FIN

AF:

0.994

Gnomad MID

AF:

0.953

Gnomad NFE

AF:

0.983

Gnomad OTH

AF:

0.930

GnomAD4 exome

AF:

0.971

AC:

1336297

AN:

1375980

Hom.:

650081

Cov.:

AF XY:

0.971

AC XY:

665997

AN XY:

685726

show subpopulations

African (AFR)

AF:

0.751

AC:

23852

AN:

31744

American (AMR)

AF:

0.972

AC:

42362

AN:

43572

Ashkenazi Jewish (ASJ)

AF:

0.995

AC:

24248

AN:

24376

East Asian (EAS)

AF:

0.892

AC:

34822

AN:

39048

South Asian (SAS)

AF:

0.948

AC:

77170

AN:

81398

European-Finnish (FIN)

AF:

0.993

AC:

49077

AN:

49436

Middle Eastern (MID)

AF:

0.967

AC:

4265

AN:

4412

European-Non Finnish (NFE)

AF:

0.982

AC:

1025676

AN:

1044628

Other (OTH)

AF:

0.956

AC:

54825

AN:

57366

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1903

3806

5709

7612

9515

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

20098

40196

60294

80392

100490

<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:

0.912

AC:

138810

AN:

152216

Hom.:

64107

Cov.:

AF XY:

0.915

AC XY:

68089

AN XY:

74428

show subpopulations

African (AFR)

AF:

0.753

AC:

31232

AN:

41476

American (AMR)

AF:

0.945

AC:

14463

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.997

AC:

3458

AN:

3470

East Asian (EAS)

AF:

0.886

AC:

4569

AN:

5154

South Asian (SAS)

AF:

0.952

AC:

4597

AN:

4830

European-Finnish (FIN)

AF:

0.994

AC:

10562

AN:

10628

Middle Eastern (MID)

AF:

0.942

AC:

277

AN:

294

European-Non Finnish (NFE)

AF:

0.983

AC:

66844

AN:

68034

Other (OTH)

AF:

0.929

AC:

1966

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

549

1099

1648

2198

2747

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

900

1800

2700

3600

4500

<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:

0.936

Hom.:

26013

Bravo

AF:

0.902

Asia WGS

AF:

0.917

AC:

3191

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.28

(source)

DANN

Benign

0.79

PhyloP100

-1.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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