dbSNP rs12957330: CNDP1:c.1458-352G>A (chr18-74584144-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.1458-352G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 325,068 control chromosomes in the GnomAD database, including 4,387 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 0.13 ( 1717 hom., cov: 33)

Exomes 𝑓: 0.16 ( 2670 hom. )

Consequence

CNDP1
NM_032649.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.918

Publications

6 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:

ZNF407-AS1 (HGNC:44331): (ZNF407 antisense RNA 1)

ZNF407-AS1 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_032649.6, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.88).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.184 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.1458-352G>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.1458-352G>A	intron	N/A	ENSP00000351682.3	Q96KN2
CNDP1	ENST00000864762.1		c.1527-352G>A	intron	N/A	ENSP00000534821.1
CNDP1	ENST00000954332.1		c.1455-352G>A	intron	N/A	ENSP00000624391.1

Frequencies

GnomAD3 genomes

AF:

0.134

AC:

20407

AN:

152074

Hom.:

1719

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0340

Gnomad AMI

AF:

0.249

Gnomad AMR

AF:

0.127

Gnomad ASJ

AF:

0.220

Gnomad EAS

AF:

0.0801

Gnomad SAS

AF:

0.162

Gnomad FIN

AF:

0.174

Gnomad MID

AF:

0.115

Gnomad NFE

AF:

0.187

Gnomad OTH

AF:

0.129

GnomAD4 exome

AF:

0.164

AC:

28308

AN:

172876

Hom.:

2670

Cov.:

AF XY:

0.162

AC XY:

14728

AN XY:

90806

show subpopulations

African (AFR)

AF:

0.0302

AC:

186

AN:

6158

American (AMR)

AF:

0.133

AC:

985

AN:

7396

Ashkenazi Jewish (ASJ)

AF:

0.231

AC:

1173

AN:

5078

East Asian (EAS)

AF:

0.0682

AC:

687

AN:

10068

South Asian (SAS)

AF:

0.152

AC:

3081

AN:

20260

European-Finnish (FIN)

AF:

0.156

AC:

1212

AN:

7746

Middle Eastern (MID)

AF:

0.120

AC:

AN:

682

European-Non Finnish (NFE)

AF:

0.183

AC:

19310

AN:

105680

Other (OTH)

AF:

0.162

AC:

1592

AN:

9808

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1096

2193

3289

4386

5482

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

136

272

408

544

680

<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:

0.134

AC:

20403

AN:

152192

Hom.:

1717

Cov.:

AF XY:

0.133

AC XY:

9923

AN XY:

74410

show subpopulations

African (AFR)

AF:

0.0339

AC:

1409

AN:

41522

American (AMR)

AF:

0.127

AC:

1944

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.220

AC:

762

AN:

3466

East Asian (EAS)

AF:

0.0799

AC:

414

AN:

5184

South Asian (SAS)

AF:

0.163

AC:

787

AN:

4820

European-Finnish (FIN)

AF:

0.174

AC:

1845

AN:

10588

Middle Eastern (MID)

AF:

0.116

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.187

AC:

12711

AN:

68000

Other (OTH)

AF:

0.128

AC:

270

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

893

1785

2678

3570

4463

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

230

460

690

920

1150

<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:

0.175

Hom.:

3963

Bravo

AF:

0.127

Asia WGS

AF:

0.0940

AC:

328

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

9.5

(source)

DANN

Benign

0.72

PhyloP100

0.92

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.10

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

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