dbSNP rs9967490: CNDP1:c.467-70G>A (chr18-74561977-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_032649.6(CNDP1):c.467-70G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 1,299,426 control chromosomes in the GnomAD database, including 60,057 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 0.35 ( 10704 hom., cov: 32)

Exomes 𝑓: 0.29 ( 49353 hom. )

Consequence

CNDP1
NM_032649.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.44

Publications

12 publications found

Variant links:

Genes affected

CNDP1 (HGNC:20675): (carnosine dipeptidase 1) This gene encodes a member of the M20 metalloprotease family. The encoded protein is specifically expressed in the brain, is a homodimeric dipeptidase which was identified as human carnosinase. This gene contains trinucleotide (CTG) repeat length polymorphism in the coding region. [provided by RefSeq, Jul 2008]

CNDP1 links:

ENSG00000264340 (HGNC:58557):

ENSG00000264340 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=-0.94).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032649.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNDP1	NM_032649.6	MANE Select	c.467-70G>A		intron	N/A	NP_116038.4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CNDP1	ENST00000358821.8	TSL:1 MANE Select	c.467-70G>A	intron	N/A	ENSP00000351682.3	Q96KN2
CNDP1	ENST00000864762.1		c.467-70G>A	intron	N/A	ENSP00000534821.1
CNDP1	ENST00000954332.1		c.467-70G>A	intron	N/A	ENSP00000624391.1

Frequencies

GnomAD3 genomes

AF:

0.350

AC:

53192

AN:

151934

Hom.:

10685

Cov.:

show subpopulations

Gnomad AFR

AF:

0.558

Gnomad AMI

AF:

0.196

Gnomad AMR

AF:

0.258

Gnomad ASJ

AF:

0.333

Gnomad EAS

AF:

0.126

Gnomad SAS

AF:

0.335

Gnomad FIN

AF:

0.204

Gnomad MID

AF:

0.376

Gnomad NFE

AF:

0.288

Gnomad OTH

AF:

0.337

GnomAD4 exome

AF:

0.286

AC:

328391

AN:

1147374

Hom.:

49353

Cov.:

AF XY:

0.287

AC XY:

167780

AN XY:

584492

show subpopulations

African (AFR)

AF:

0.568

AC:

15494

AN:

27302

American (AMR)

AF:

0.186

AC:

8075

AN:

43334

Ashkenazi Jewish (ASJ)

AF:

0.336

AC:

8032

AN:

23880

East Asian (EAS)

AF:

0.119

AC:

4500

AN:

37906

South Asian (SAS)

AF:

0.323

AC:

25500

AN:

78988

European-Finnish (FIN)

AF:

0.212

AC:

10987

AN:

51842

Middle Eastern (MID)

AF:

0.354

AC:

1827

AN:

5154

European-Non Finnish (NFE)

AF:

0.288

AC:

238759

AN:

829234

Other (OTH)

AF:

0.306

AC:

15217

AN:

49734

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

11362

22724

34086

45448

56810

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7018

14036

21054

28072

35090

<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:

0.350

AC:

53250

AN:

152052

Hom.:

10704

Cov.:

AF XY:

0.344

AC XY:

25604

AN XY:

74326

show subpopulations

African (AFR)

AF:

0.559

AC:

23160

AN:

41466

American (AMR)

AF:

0.258

AC:

3929

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.333

AC:

1157

AN:

3470

East Asian (EAS)

AF:

0.126

AC:

654

AN:

5178

South Asian (SAS)

AF:

0.334

AC:

1610

AN:

4824

European-Finnish (FIN)

AF:

0.204

AC:

2158

AN:

10556

Middle Eastern (MID)

AF:

0.380

AC:

111

AN:

292

European-Non Finnish (NFE)

AF:

0.288

AC:

19592

AN:

67994

Other (OTH)

AF:

0.332

AC:

701

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1641

3282

4923

6564

8205

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

504

1008

1512

2016

2520

<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:

0.303

Hom.:

12887

Bravo

AF:

0.362

Asia WGS

AF:

0.227

AC:

789

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.0020

(source)

DANN

Benign

0.38

PhyloP100

-3.4

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