dbSNP rs12605490: CNDP1:c.154-103A>T (chr18-74559220-A-T) – 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.154-103A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.784 in 1,172,228 control chromosomes in the GnomAD database, including 363,163 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 0.75 ( 43387 hom., cov: 31)

Exomes 𝑓: 0.79 ( 319776 hom. )

Consequence

CNDP1
NM_032649.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.971

Publications

5 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:

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=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.91 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNDP1	NM_032649.6	MANE Select	c.154-103A>T		intron	N/A	NP_116038.4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CNDP1	ENST00000358821.8	TSL:1 MANE Select	c.154-103A>T	intron	N/A	ENSP00000351682.3
CNDP1	ENST00000582365.1	TSL:5	c.25-103A>T	intron	N/A	ENSP00000462096.1
CNDP1	ENST00000585136.1	TSL:3	n.319-103A>T	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.747

AC:

113433

AN:

151910

Hom.:

43357

Cov.:

show subpopulations

Gnomad AFR

AF:

0.575

Gnomad AMI

AF:

0.879

Gnomad AMR

AF:

0.831

Gnomad ASJ

AF:

0.826

Gnomad EAS

AF:

0.932

Gnomad SAS

AF:

0.754

Gnomad FIN

AF:

0.859

Gnomad MID

AF:

0.750

Gnomad NFE

AF:

0.793

Gnomad OTH

AF:

0.767

GnomAD4 exome

AF:

0.790

AC:

805679

AN:

1020200

Hom.:

319776

AF XY:

0.790

AC XY:

415610

AN XY:

526416

show subpopulations

African (AFR)

AF:

0.559

AC:

13614

AN:

24368

American (AMR)

AF:

0.882

AC:

34010

AN:

38548

Ashkenazi Jewish (ASJ)

AF:

0.815

AC:

18487

AN:

22672

East Asian (EAS)

AF:

0.940

AC:

35267

AN:

37538

South Asian (SAS)

AF:

0.756

AC:

56830

AN:

75144

European-Finnish (FIN)

AF:

0.848

AC:

40056

AN:

47226

Middle Eastern (MID)

AF:

0.763

AC:

3007

AN:

3940

European-Non Finnish (NFE)

AF:

0.784

AC:

568835

AN:

725286

Other (OTH)

AF:

0.782

AC:

35573

AN:

45478

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

8492

16984

25475

33967

42459

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10886

21772

32658

43544

54430

<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:

0.747

AC:

113504

AN:

152028

Hom.:

43387

Cov.:

AF XY:

0.753

AC XY:

55939

AN XY:

74322

show subpopulations

African (AFR)

AF:

0.575

AC:

23812

AN:

41422

American (AMR)

AF:

0.831

AC:

12710

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.826

AC:

2869

AN:

3472

East Asian (EAS)

AF:

0.932

AC:

4809

AN:

5160

South Asian (SAS)

AF:

0.754

AC:

3628

AN:

4812

European-Finnish (FIN)

AF:

0.859

AC:

9098

AN:

10588

Middle Eastern (MID)

AF:

0.752

AC:

221

AN:

294

European-Non Finnish (NFE)

AF:

0.793

AC:

53934

AN:

67972

Other (OTH)

AF:

0.769

AC:

1621

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1367

2734

4101

5468

6835

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

846

1692

2538

3384

4230

<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:

0.763

Hom.:

5536

Bravo

AF:

0.738

Asia WGS

AF:

0.849

AC:

2951

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.63

(source)

DANN

Benign

0.54

PhyloP100

-0.97

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