dbSNP rs2241511: CNDP2:c.743-71G>A (chr18-74513488-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.743-71G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 1,452,442 control chromosomes in the GnomAD database, including 148,222 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 0.43 ( 14210 hom., cov: 34)

Exomes 𝑓: 0.45 ( 134012 hom. )

Consequence

CNDP2
NM_018235.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.846

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:

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=-0.96).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.646 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	UniProt
CNDP2	NM_018235.3	MANE Select	c.743-71G>A	intron	N/A	NP_060705.2	Q96KP4-1
CNDP2	NM_001370248.1		c.743-71G>A	intron	N/A	NP_001357177.1	Q96KP4-1
CNDP2	NM_001370249.1		c.743-71G>A	intron	N/A	NP_001357178.1	Q96KP4-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CNDP2	ENST00000324262.9	TSL:1 MANE Select	c.743-71G>A	intron	N/A	ENSP00000325548.4	Q96KP4-1
CNDP2	ENST00000324301.12	TSL:1	c.491-71G>A	intron	N/A	ENSP00000325756.8	Q96KP4-2
CNDP2	ENST00000880651.1		c.860-71G>A	intron	N/A	ENSP00000550710.1

Frequencies

GnomAD3 genomes

AF:

0.426

AC:

64813

AN:

152014

Hom.:

14200

Cov.:

show subpopulations

Gnomad AFR

AF:

0.333

Gnomad AMI

AF:

0.507

Gnomad AMR

AF:

0.449

Gnomad ASJ

AF:

0.542

Gnomad EAS

AF:

0.665

Gnomad SAS

AF:

0.466

Gnomad FIN

AF:

0.438

Gnomad MID

AF:

0.491

Gnomad NFE

AF:

0.448

Gnomad OTH

AF:

0.427

GnomAD4 exome

AF:

0.451

AC:

587035

AN:

1300310

Hom.:

134012

AF XY:

0.451

AC XY:

287034

AN XY:

636190

show subpopulations

African (AFR)

AF:

0.331

AC:

9595

AN:

29000

American (AMR)

AF:

0.470

AC:

13247

AN:

28212

Ashkenazi Jewish (ASJ)

AF:

0.551

AC:

11057

AN:

20054

East Asian (EAS)

AF:

0.664

AC:

23126

AN:

34838

South Asian (SAS)

AF:

0.457

AC:

31052

AN:

67974

European-Finnish (FIN)

AF:

0.454

AC:

16055

AN:

35334

Middle Eastern (MID)

AF:

0.450

AC:

2074

AN:

4612

European-Non Finnish (NFE)

AF:

0.444

AC:

455216

AN:

1026046

Other (OTH)

AF:

0.472

AC:

25613

AN:

54240

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

15191

30382

45572

60763

75954

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

14230

28460

42690

56920

71150

<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:

0.426

AC:

64852

AN:

152132

Hom.:

14210

Cov.:

AF XY:

0.429

AC XY:

31870

AN XY:

74344

show subpopulations

African (AFR)

AF:

0.333

AC:

13806

AN:

41508

American (AMR)

AF:

0.448

AC:

6861

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.542

AC:

1878

AN:

3468

East Asian (EAS)

AF:

0.665

AC:

3429

AN:

5158

South Asian (SAS)

AF:

0.466

AC:

2252

AN:

4828

European-Finnish (FIN)

AF:

0.438

AC:

4635

AN:

10572

Middle Eastern (MID)

AF:

0.486

AC:

143

AN:

294

European-Non Finnish (NFE)

AF:

0.448

AC:

30476

AN:

67984

Other (OTH)

AF:

0.432

AC:

912

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1963

3926

5888

7851

9814

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

620

1240

1860

2480

3100

<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:

0.430

Hom.:

2122

Bravo

AF:

0.424

Asia WGS

AF:

0.537

AC:

1864

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.66

(source)

DANN

Benign

0.63

PhyloP100

-0.85

Mutation Taster

=4/96

disease causing

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

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