Variant rs12605520 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.154-54C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 1,596,032 control chromosomes in the GnomAD database, including 98,464 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 0.30 ( 7693 hom., cov: 32)

Exomes 𝑓: 0.35 ( 90771 hom. )

Consequence

CNDP1
NM_032649.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.661

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=-0.81).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CNDP1	NM_032649.6 linkuse as main transcript	c.154-54C>T		intron_variant		ENST00000358821.8	NP_116038.4

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris
CNDP1	ENST00000358821.8 linkuse as main transcript	c.154-54C>T	intron_variant	1	NM_032649.6	ENSP00000351682	P1
CNDP1	ENST00000582365.1 linkuse as main transcript	c.25-54C>T	intron_variant	5		ENSP00000462096
CNDP1	ENST00000585136.1 linkuse as main transcript	n.319-54C>T	intron_variant, non_coding_transcript_variant	3

Frequencies

GnomAD3 genomes

AF:

0.302

AC:

45912

AN:

152018

Hom.:

7691

Cov.:

show subpopulations

Gnomad AFR

AF:

0.156

Gnomad AMI

AF:

0.363

Gnomad AMR

AF:

0.322

Gnomad ASJ

AF:

0.434

Gnomad EAS

AF:

0.436

Gnomad SAS

AF:

0.384

Gnomad FIN

AF:

0.341

Gnomad MID

AF:

0.389

Gnomad NFE

AF:

0.355

Gnomad OTH

AF:

0.349

GnomAD4 exome

AF:

0.351

AC:

506640

AN:

1443896

Hom.:

90771

AF XY:

0.353

AC XY:

254264

AN XY:

719354

show subpopulations

Gnomad4 AFR exome

AF:

0.148

Gnomad4 AMR exome

AF:

0.337

Gnomad4 ASJ exome

AF:

0.439

Gnomad4 EAS exome

AF:

0.391

Gnomad4 SAS exome

AF:

0.388

Gnomad4 FIN exome

AF:

0.351

Gnomad4 NFE exome

AF:

0.350

Gnomad4 OTH exome

AF:

0.356

GnomAD4 genome

AF:

0.302

AC:

45933

AN:

152136

Hom.:

7693

Cov.:

AF XY:

0.306

AC XY:

22727

AN XY:

74346

show subpopulations

Gnomad4 AFR

AF:

0.156

Gnomad4 AMR

AF:

0.323

Gnomad4 ASJ

AF:

0.434

Gnomad4 EAS

AF:

0.436

Gnomad4 SAS

AF:

0.385

Gnomad4 FIN

AF:

0.341

Gnomad4 NFE

AF:

0.355

Gnomad4 OTH

AF:

0.352

Alfa

AF:

0.357

Hom.:

13094

Bravo

AF:

0.295

Asia WGS

AF:

0.395

AC:

1370

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

0.47

DANN

Benign

0.57

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