Variant 18-74501372-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_018235.3(CNDP2):c.104C>T(p.Pro35Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00319 in 1,613,924 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0022 ( 0 hom., cov: 33)

Exomes 𝑓: 0.0033 ( 18 hom. )

Consequence

CNDP2
NM_018235.3 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 7.79

Variant links:

Genes affected

CNDP2 (HGNC:24437): (carnosine dipeptidase 2) CNDP2, also known as tissue carnosinase and peptidase A (EC 3.4.13.18), is a nonspecific dipeptidase rather than a selective carnosinase (Teufel et al., 2003 [PubMed 12473676]).[supplied by OMIM, Mar 2008]

CNDP2 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=0.011466712).

BP6

Variant 18-74501372-C-T is Benign according to our data. Variant chr18-74501372-C-T is described in ClinVar as [Benign]. Clinvar id is 788917.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 18 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CNDP2	NM_018235.3 linkuse as main transcript	c.104C>T	p.Pro35Leu	missense_variant	3/12	ENST00000324262.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CNDP2	ENST00000324262.9 linkuse as main transcript	c.104C>T	p.Pro35Leu	missense_variant	3/12	1	NM_018235.3	P1	Q96KP4-1

Frequencies

GnomAD3 genomes

AF:

0.00217

AC:

330

AN:

152026

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000387

Gnomad AMI

AF:

0.00329

Gnomad AMR

AF:

0.000917

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00893

Gnomad FIN

AF:

0.00529

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00285

Gnomad OTH

AF:

0.000956

GnomAD3 exomes

AF:

0.00273

AC:

687

AN:

251402

Hom.:

AF XY:

0.00298

AC XY:

405

AN XY:

135876

show subpopulations

Gnomad AFR exome

AF:

0.000246

Gnomad AMR exome

AF:

0.00168

Gnomad ASJ exome

AF:

0.0000993

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00650

Gnomad FIN exome

AF:

0.00430

Gnomad NFE exome

AF:

0.00279

Gnomad OTH exome

AF:

0.00244

GnomAD4 exome

AF:

0.00329

AC:

4813

AN:

1461780

Hom.:

Cov.:

AF XY:

0.00343

AC XY:

2494

AN XY:

727198

show subpopulations

Gnomad4 AFR exome

AF:

0.000209

Gnomad4 AMR exome

AF:

0.00163

Gnomad4 ASJ exome

AF:

0.000115

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00677

Gnomad4 FIN exome

AF:

0.00500

Gnomad4 NFE exome

AF:

0.00336

Gnomad4 OTH exome

AF:

0.00220

GnomAD4 genome

AF:

0.00217

AC:

330

AN:

152144

Hom.:

Cov.:

AF XY:

0.00235

AC XY:

175

AN XY:

74360

show subpopulations

Gnomad4 AFR

AF:

0.000386

Gnomad4 AMR

AF:

0.000916

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00894

Gnomad4 FIN

AF:

0.00529

Gnomad4 NFE

AF:

0.00285

Gnomad4 OTH

AF:

0.000946

Alfa

AF:

0.00252

Hom.:

Bravo

AF:

0.00183

TwinsUK

AF:

0.00593

AC:

ALSPAC

AF:

0.00363

AC:

ESP6500AA

AF:

0.000454

AC:

ESP6500EA

AF:

0.00372

AC:

ExAC

AF:

0.00292

AC:

354

Asia WGS

AF:

0.00318

AC:

AN:

3478

EpiCase

AF:

0.00284

EpiControl

AF:

0.00362

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

Jul 03, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.26

BayesDel_addAF

Benign

-0.10

BayesDel_noAF

Uncertain

0.080

CADD

Pathogenic

DANN

Benign

0.96

DEOGEN2

Benign

0.087

T;T;T;T;.;T;.;T;T;.;T;T;.;.

Eigen

Uncertain

0.53

Eigen_PC

Uncertain

0.55

FATHMM_MKL

Uncertain

0.96

LIST_S2

Pathogenic

0.99

D;.;D;D;D;D;D;D;D;D;D;D;D;D

MetaRNN

Benign

0.011

T;T;T;T;T;T;T;T;T;T;T;T;T;T

MetaSVM

Benign

-1.1

MutationTaster

Benign

1.0

D;D;D

PrimateAI

Uncertain

0.61

Sift4G

Benign

0.094

T;T;T;D;T;D;T;T;T;D;T;T;T;T

Polyphen

0.43, 1.0

.;B;B;.;.;.;.;.;.;.;.;.;D;.

Vest4

0.85, 0.89, 0.82

MVP

0.90

MPC

0.22

ClinPred

0.095

GERP RS

5.8

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.50

gMVP

0.76

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over