Variant chr18-74580042-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_032649.6(CNDP1):c.1168-88C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.678 in 1,164,230 control chromosomes in the GnomAD database, including 269,221 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 0.67 ( 34303 hom., cov: 33)

Exomes 𝑓: 0.68 ( 234918 hom. )

Consequence

CNDP1
NM_032649.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0330

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 made for transcript

Verdict is Benign. Variant got -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 = 0.777 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CNDP1	NM_032649.6 link	c.1168-88C>T		intron_variant		ENST00000358821.8	NP_116038.4	Q96KN2

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
CNDP1	ENST00000358821.8 link	c.1168-88C>T	intron_variant	1	NM_032649.6	ENSP00000351682.3	Q96KN2
CNDP1	ENST00000582365.1 link	c.1039-88C>T	intron_variant	5		ENSP00000462096.1	J3KRP0
CNDP1	ENST00000582461.1 link	n.2049-88C>T	intron_variant	5
CNDP1	ENST00000584004.5 link	n.692-88C>T	intron_variant	2

Frequencies

GnomAD3 genomes

AF:

0.669

AC:

101608

AN:

151988

Hom.:

34264

Cov.:

show subpopulations

Gnomad AFR

AF:

0.618

Gnomad AMI

AF:

0.651

Gnomad AMR

AF:

0.762

Gnomad ASJ

AF:

0.656

Gnomad EAS

AF:

0.797

Gnomad SAS

AF:

0.759

Gnomad FIN

AF:

0.680

Gnomad MID

AF:

0.709

Gnomad NFE

AF:

0.660

Gnomad OTH

AF:

0.693

GnomAD4 exome

AF:

0.679

AC:

687609

AN:

1012124

Hom.:

234918

AF XY:

0.681

AC XY:

349772

AN XY:

513350

show subpopulations

Gnomad4 AFR exome

AF:

0.613

Gnomad4 AMR exome

AF:

0.797

Gnomad4 ASJ exome

AF:

0.645

Gnomad4 EAS exome

AF:

0.822

Gnomad4 SAS exome

AF:

0.757

Gnomad4 FIN exome

AF:

0.681

Gnomad4 NFE exome

AF:

0.663

Gnomad4 OTH exome

AF:

0.681

GnomAD4 genome

AF:

0.669

AC:

101701

AN:

152106

Hom.:

34303

Cov.:

AF XY:

0.674

AC XY:

50113

AN XY:

74362

show subpopulations

Gnomad4 AFR

AF:

0.619

Gnomad4 AMR

AF:

0.763

Gnomad4 ASJ

AF:

0.656

Gnomad4 EAS

AF:

0.798

Gnomad4 SAS

AF:

0.758

Gnomad4 FIN

AF:

0.680

Gnomad4 NFE

AF:

0.660

Gnomad4 OTH

AF:

0.698

Alfa

AF:

0.654

Hom.:

4075

Bravo

AF:

0.675

Asia WGS

AF:

0.792

AC:

2755

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.70

DANN

Benign

0.17

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over