Variant 18-74567390-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_032649.6(CNDP1):c.713C>T(p.Ala238Val) variant causes a missense change. The variant allele was found at a frequency of 0.00374 in 1,614,098 control chromosomes in the GnomAD database, including 25 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0037 ( 2 hom., cov: 33)

Exomes 𝑓: 0.0037 ( 23 hom. )

Consequence

CNDP1
NM_032649.6 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.87

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 -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.012044758).

BP6

Variant 18-74567390-C-T is Benign according to our data. Variant chr18-74567390-C-T is described in ClinVar as [Benign]. Clinvar id is 735260.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr18-74567390-C-T is described in Lovd as [Benign].

BS2

High Homozygotes in GnomAd at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CNDP1	NM_032649.6 linkuse as main transcript	c.713C>T	p.Ala238Val	missense_variant	6/12	ENST00000358821.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
CNDP1	ENST00000358821.8 linkuse as main transcript	c.713C>T	p.Ala238Val	missense_variant	6/12	1	NM_032649.6	P1
CNDP1	ENST00000582365.1 linkuse as main transcript	c.584C>T	p.Ala195Val	missense_variant	5/11	5
CNDP1	ENST00000584004.5 linkuse as main transcript	n.237C>T		non_coding_transcript_exon_variant	1/7	2
CNDP1	ENST00000584316.5 linkuse as main transcript	c.*181C>T		3_prime_UTR_variant, NMD_transcript_variant	3/5	4

Frequencies

GnomAD3 genomes

AF:

0.00371

AC:

564

AN:

152186

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000676

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00334

Gnomad ASJ

AF:

0.0182

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00373

Gnomad FIN

AF:

0.00264

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.00531

Gnomad OTH

AF:

0.00574

GnomAD3 exomes

AF:

0.00444

AC:

1117

AN:

251370

Hom.:

AF XY:

0.00458

AC XY:

622

AN XY:

135854

show subpopulations

Gnomad AFR exome

AF:

0.000861

Gnomad AMR exome

AF:

0.00324

Gnomad ASJ exome

AF:

0.0127

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00496

Gnomad FIN exome

AF:

0.00296

Gnomad NFE exome

AF:

0.00544

Gnomad OTH exome

AF:

0.00473

GnomAD4 exome

AF:

0.00374

AC:

5474

AN:

1461794

Hom.:

Cov.:

AF XY:

0.00385

AC XY:

2797

AN XY:

727198

show subpopulations

Gnomad4 AFR exome

AF:

0.000418

Gnomad4 AMR exome

AF:

0.00360

Gnomad4 ASJ exome

AF:

0.0134

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00499

Gnomad4 FIN exome

AF:

0.00275

Gnomad4 NFE exome

AF:

0.00365

Gnomad4 OTH exome

AF:

0.00449

GnomAD4 genome

AF:

0.00370

AC:

563

AN:

152304

Hom.:

Cov.:

AF XY:

0.00359

AC XY:

267

AN XY:

74464

show subpopulations

Gnomad4 AFR

AF:

0.000674

Gnomad4 AMR

AF:

0.00333

Gnomad4 ASJ

AF:

0.0182

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00373

Gnomad4 FIN

AF:

0.00264

Gnomad4 NFE

AF:

0.00531

Gnomad4 OTH

AF:

0.00521

Alfa

AF:

0.00509

Hom.:

Bravo

AF:

0.00353

TwinsUK

AF:

0.00431

AC:

ALSPAC

AF:

0.00259

AC:

ESP6500AA

AF:

0.000908

AC:

ESP6500EA

AF:

0.00616

AC:

ExAC

AF:

0.00451

AC:

547

Asia WGS

AF:

0.000866

AC:

AN:

3478

EpiCase

AF:

0.00567

EpiControl

AF:

0.00688

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.31

BayesDel_addAF

Benign

-0.46

BayesDel_noAF

Benign

-0.43

Cadd

Benign

Dann

Uncertain

1.0

Eigen

Uncertain

0.41

Eigen_PC

Uncertain

0.32

FATHMM_MKL

Uncertain

0.91

M_CAP

Benign

0.019

MetaRNN

Benign

0.012

T;T

MetaSVM

Benign

-1.1

MutationTaster

Benign

0.92

N;N

PrimateAI

Benign

0.41

PROVEAN

Uncertain

-2.4

N;.

REVEL

Benign

0.22

Sift

Benign

0.18

T;.

Sift4G

Benign

0.15

T;T

Vest4

0.66

MVP

0.57

MPC

0.62

ClinPred

0.027

GERP RS

5.3

gMVP

0.37

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over