Genetic Variant CNDP2:c.-85C>G (chr18-74499889-C-G) – 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.-85C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 1,255,076 control chromosomes in the GnomAD database, including 49,791 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 0.32 ( 8994 hom., cov: 32)

Exomes 𝑓: 0.27 ( 40797 hom. )

Consequence

CNDP2
NM_018235.3 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.95

Publications

30 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=-0.86).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.488 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.-85C>G	5_prime_UTR	Exon 2 of 12	NP_060705.2	Q96KP4-1
CNDP2	NM_001370254.1		c.-1022C>G	5_prime_UTR	Exon 2 of 12	NP_001357183.1
CNDP2	NM_001370248.1		c.-37-48C>G	intron	N/A	NP_001357177.1	Q96KP4-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CNDP2	ENST00000324262.9	TSL:1 MANE Select	c.-85C>G	5_prime_UTR	Exon 2 of 12	ENSP00000325548.4	Q96KP4-1
CNDP2	ENST00000324301.12	TSL:1	c.-85C>G	5_prime_UTR	Exon 1 of 9	ENSP00000325756.8	Q96KP4-2
CNDP2	ENST00000880651.1		c.-85C>G	5_prime_UTR	Exon 2 of 12	ENSP00000550710.1

Frequencies

GnomAD3 genomes

AF:

0.325

AC:

49335

AN:

151954

Hom.:

8978

Cov.:

show subpopulations

Gnomad AFR

AF:

0.494

Gnomad AMI

AF:

0.302

Gnomad AMR

AF:

0.352

Gnomad ASJ

AF:

0.217

Gnomad EAS

AF:

0.288

Gnomad SAS

AF:

0.339

Gnomad FIN

AF:

0.172

Gnomad MID

AF:

0.241

Gnomad NFE

AF:

0.248

Gnomad OTH

AF:

0.315

GnomAD4 exome

AF:

0.266

AC:

293193

AN:

1103004

Hom.:

40797

Cov.:

AF XY:

0.267

AC XY:

150336

AN XY:

562738

show subpopulations

African (AFR)

AF:

0.501

AC:

12553

AN:

25068

American (AMR)

AF:

0.376

AC:

12715

AN:

33802

Ashkenazi Jewish (ASJ)

AF:

0.220

AC:

4804

AN:

21790

East Asian (EAS)

AF:

0.298

AC:

10949

AN:

36778

South Asian (SAS)

AF:

0.330

AC:

24215

AN:

73274

European-Finnish (FIN)

AF:

0.175

AC:

9096

AN:

51876

Middle Eastern (MID)

AF:

0.262

AC:

1300

AN:

4970

European-Non Finnish (NFE)

AF:

0.254

AC:

204762

AN:

807488

Other (OTH)

AF:

0.267

AC:

12799

AN:

47958

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

10251

20502

30753

41004

51255

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6470

12940

19410

25880

32350

<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:

0.325

AC:

49386

AN:

152072

Hom.:

8994

Cov.:

AF XY:

0.324

AC XY:

24079

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.494

AC:

20452

AN:

41440

American (AMR)

AF:

0.353

AC:

5395

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.217

AC:

752

AN:

3468

East Asian (EAS)

AF:

0.288

AC:

1490

AN:

5176

South Asian (SAS)

AF:

0.338

AC:

1628

AN:

4822

European-Finnish (FIN)

AF:

0.172

AC:

1824

AN:

10602

Middle Eastern (MID)

AF:

0.241

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.248

AC:

16834

AN:

67960

Other (OTH)

AF:

0.314

AC:

665

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1594

3189

4783

6378

7972

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

478

956

1434

1912

2390

<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:

0.147

Hom.:

250

Bravo

AF:

0.344

Asia WGS

AF:

0.343

AC:

1195

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.24

(source)

DANN

Benign

0.44

PhyloP100

-2.9

PromoterAI

0.27

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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