dbSNP rs17089362: CNDP2:c.1069-96G>A (chr18-74518403-G-A) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_018235.3(CNDP2):c.1069-96G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00104 in 1,434,144 control chromosomes in the GnomAD database, including 1 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 0.0020 ( 0 hom., cov: 33)

Exomes 𝑓: 0.00093 ( 1 hom. )

Consequence

CNDP2
NM_018235.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.17

Publications

3 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: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

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.1069-96G>A	intron	N/A	NP_060705.2
CNDP2	NM_001370248.1		c.1069-96G>A	intron	N/A	NP_001357177.1
CNDP2	NM_001370249.1		c.1069-96G>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.1069-96G>A	intron	N/A	ENSP00000325548.4
CNDP2	ENST00000324301.12	TSL:1	c.817-96G>A	intron	N/A	ENSP00000325756.8
CNDP2	ENST00000880651.1		c.1186-96G>A	intron	N/A	ENSP00000550710.1

Frequencies

GnomAD3 genomes

AF:

0.00199

AC:

303

AN:

152164

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00418

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00301

Gnomad ASJ

AF:

0.00576

Gnomad EAS

AF:

0.000963

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.000705

Gnomad OTH

AF:

0.00335

GnomAD4 exome

AF:

0.000929

AC:

1191

AN:

1281862

Hom.:

Cov.:

AF XY:

0.000933

AC XY:

597

AN XY:

639744

show subpopulations

African (AFR)

AF:

0.00434

AC:

130

AN:

29934

American (AMR)

AF:

0.00317

AC:

132

AN:

41584

Ashkenazi Jewish (ASJ)

AF:

0.00709

AC:

160

AN:

22564

East Asian (EAS)

AF:

0.00171

AC:

AN:

38498

South Asian (SAS)

AF:

0.000131

AC:

AN:

76238

European-Finnish (FIN)

AF:

0.000184

AC:

AN:

48818

Middle Eastern (MID)

AF:

0.00326

AC:

AN:

5220

European-Non Finnish (NFE)

AF:

0.000577

AC:

557

AN:

965070

Other (OTH)

AF:

0.00204

AC:

110

AN:

53936

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

116

174

232

290

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

110

<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:

0.00200

AC:

304

AN:

152282

Hom.:

Cov.:

AF XY:

0.00212

AC XY:

158

AN XY:

74468

show subpopulations

African (AFR)

AF:

0.00419

AC:

174

AN:

41538

American (AMR)

AF:

0.00301

AC:

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.00576

AC:

AN:

3472

East Asian (EAS)

AF:

0.000965

AC:

AN:

5180

South Asian (SAS)

AF:

0.00

AC:

AN:

4824

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10614

Middle Eastern (MID)

AF:

0.0136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000706

AC:

AN:

68036

Other (OTH)

AF:

0.00331

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

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

Alfa

AF:

0.00000458

Hom.:

134

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.0010

(source)

DANN

Benign

0.59

PhyloP100

-2.2

Mutation Taster

=100/0

polymorphism

(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