Genetic Variant CNDP2:p.Gly26Arg (chr18-74496357-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 ENST00000580672.5(CNDP2):c.76G>A(p.Gly26Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 152,208 control chromosomes in the GnomAD database, including 13,041 homozygotes. In-silico tool predicts a benign outcome for this variant. 9/12 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.41 ( 13026 hom., cov: 33)

Exomes 𝑓: 0.40 ( 15 hom. )

Consequence

CNDP2
ENST00000580672.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.267

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 (MetaRNN=1.0119554E-6).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000580672.5. 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.-167G>A	upstream_gene	N/A	NP_060705.2
CNDP2	NM_001370248.1		c.-112G>A	upstream_gene	N/A	NP_001357177.1
CNDP2	NM_001370249.1		c.-434G>A	upstream_gene	N/A	NP_001357178.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
CNDP2	ENST00000580672.5	TSL:5	c.76G>A	p.Gly26Arg	missense	Exon 1 of 5	ENSP00000464214.1
CNDP2	ENST00000582260.5	TSL:5	n.-112G>A		non_coding_transcript_exon	Exon 1 of 6	ENSP00000464319.1
CNDP2	ENST00000583399.5	TSL:2	n.51G>A		non_coding_transcript_exon	Exon 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.408

AC:

62065

AN:

151934

Hom.:

13016

Cov.:

show subpopulations

Gnomad AFR

AF:

0.336

Gnomad AMI

AF:

0.501

Gnomad AMR

AF:

0.424

Gnomad ASJ

AF:

0.534

Gnomad EAS

AF:

0.684

Gnomad SAS

AF:

0.440

Gnomad FIN

AF:

0.373

Gnomad MID

AF:

0.516

Gnomad NFE

AF:

0.423

Gnomad OTH

AF:

0.408

GnomAD2 exomes

AF:

0.477

AC:

453

AN:

950

AF XY:

0.500

show subpopulations

Gnomad ASJ exome

AF:

1.00

Gnomad NFE exome

AF:

0.477

Gnomad OTH exome

AF:

0.333

GnomAD4 exome

AF:

0.404

AC:

AN:

156

Hom.:

Cov.:

AF XY:

0.392

AC XY:

AN XY:

120

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.750

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.403

AC:

AN:

134

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.551

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

Variant carriers

<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:

0.408

AC:

62098

AN:

152052

Hom.:

13026

Cov.:

AF XY:

0.409

AC XY:

30422

AN XY:

74332

show subpopulations

African (AFR)

AF:

0.336

AC:

13958

AN:

41500

American (AMR)

AF:

0.423

AC:

6473

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.534

AC:

1850

AN:

3466

East Asian (EAS)

AF:

0.683

AC:

3514

AN:

5142

South Asian (SAS)

AF:

0.441

AC:

2123

AN:

4818

European-Finnish (FIN)

AF:

0.373

AC:

3954

AN:

10588

Middle Eastern (MID)

AF:

0.514

AC:

150

AN:

292

European-Non Finnish (NFE)

AF:

0.423

AC:

28752

AN:

67934

Other (OTH)

AF:

0.412

AC:

872

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1904

3808

5712

7616

9520

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

600

1200

1800

2400

3000

<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:

0.417

Hom.:

28691

Bravo

AF:

0.411

TwinsUK

AF:

0.422

AC:

1563

ALSPAC

AF:

0.427

AC:

1645

ExAC

AF:

0.158

AC:

404

Asia WGS

AF:

0.517

AC:

1793

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.22

BayesDel_addAF

Benign

-0.70

BayesDel_noAF

Benign

-0.63

CADD

Benign

(source)

DANN

Benign

0.85

FATHMM_MKL

Benign

0.0054

LIST_S2

Benign

0.27

MetaRNN

Benign

0.0000010

PhyloP100

0.27

PrimateAI

Uncertain

0.61

Sift4G

Benign

0.13

GERP RS

-5.6

PromoterAI

-0.027

Neutral

(source)

Mutation Taster

=300/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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