Variant chr18-74559574-C-A 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.303+102C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 1,061,876 control chromosomes in the GnomAD database, including 75,646 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 0.39 ( 11738 hom., cov: 31)

Exomes 𝑓: 0.37 ( 63908 hom. )

Consequence

CNDP1
NM_032649.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0520

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=-0.91).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.435 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.303+102C>A		intron_variant		ENST00000358821.8	NP_116038.4

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris
CNDP1	ENST00000358821.8 linkuse as main transcript	c.303+102C>A	intron_variant	1	NM_032649.6	ENSP00000351682	P1
CNDP1	ENST00000582365.1 linkuse as main transcript	c.174+102C>A	intron_variant	5		ENSP00000462096
CNDP1	ENST00000585136.1 linkuse as main transcript	n.468+102C>A	intron_variant, non_coding_transcript_variant	3

Frequencies

GnomAD3 genomes

AF:

0.391

AC:

59313

AN:

151826

Hom.:

11727

Cov.:

show subpopulations

Gnomad AFR

AF:

0.412

Gnomad AMI

AF:

0.427

Gnomad AMR

AF:

0.444

Gnomad ASJ

AF:

0.350

Gnomad EAS

AF:

0.373

Gnomad SAS

AF:

0.314

Gnomad FIN

AF:

0.455

Gnomad MID

AF:

0.282

Gnomad NFE

AF:

0.365

Gnomad OTH

AF:

0.356

GnomAD4 exome

AF:

0.369

AC:

335448

AN:

909934

Hom.:

63908

AF XY:

0.366

AC XY:

167226

AN XY:

457192

show subpopulations

Gnomad4 AFR exome

AF:

0.409

Gnomad4 AMR exome

AF:

0.465

Gnomad4 ASJ exome

AF:

0.334

Gnomad4 EAS exome

AF:

0.455

Gnomad4 SAS exome

AF:

0.307

Gnomad4 FIN exome

AF:

0.437

Gnomad4 NFE exome

AF:

0.364

Gnomad4 OTH exome

AF:

0.361

GnomAD4 genome

AF:

0.391

AC:

59355

AN:

151942

Hom.:

11738

Cov.:

AF XY:

0.391

AC XY:

29025

AN XY:

74250

show subpopulations

Gnomad4 AFR

AF:

0.412

Gnomad4 AMR

AF:

0.444

Gnomad4 ASJ

AF:

0.350

Gnomad4 EAS

AF:

0.374

Gnomad4 SAS

AF:

0.313

Gnomad4 FIN

AF:

0.455

Gnomad4 NFE

AF:

0.365

Gnomad4 OTH

AF:

0.357

Alfa

AF:

0.368

Hom.:

4493

Bravo

AF:

0.391

Asia WGS

AF:

0.377

AC:

1312

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.35

DANN

Benign

0.70

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