Variant rs2278161 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_018235.3(CNDP2):c.376T>C(p.Tyr126His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.227 in 1,612,658 control chromosomes in the GnomAD database, including 43,585 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. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.20 ( 3288 hom., cov: 32)

Exomes 𝑓: 0.23 ( 40297 hom. )

Consequence

CNDP2
NM_018235.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 7.65

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 -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.002690345).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CNDP2	NM_018235.3 linkuse as main transcript	c.376T>C	p.Tyr126His	missense_variant	5/12	ENST00000324262.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CNDP2	ENST00000324262.9 linkuse as main transcript	c.376T>C	p.Tyr126His	missense_variant	5/12	1	NM_018235.3	P1	Q96KP4-1

Frequencies

GnomAD3 genomes

AF:

0.197

AC:

29934

AN:

151916

Hom.:

3279

Cov.:

show subpopulations

Gnomad AFR

AF:

0.114

Gnomad AMI

AF:

0.270

Gnomad AMR

AF:

0.292

Gnomad ASJ

AF:

0.169

Gnomad EAS

AF:

0.290

Gnomad SAS

AF:

0.263

Gnomad FIN

AF:

0.133

Gnomad MID

AF:

0.193

Gnomad NFE

AF:

0.224

Gnomad OTH

AF:

0.208

GnomAD3 exomes

AF:

0.232

AC:

58365

AN:

251346

Hom.:

7413

AF XY:

0.232

AC XY:

31554

AN XY:

135860

show subpopulations

Gnomad AFR exome

AF:

0.115

Gnomad AMR exome

AF:

0.350

Gnomad ASJ exome

AF:

0.166

Gnomad EAS exome

AF:

0.299

Gnomad SAS exome

AF:

0.259

Gnomad FIN exome

AF:

0.134

Gnomad NFE exome

AF:

0.220

Gnomad OTH exome

AF:

0.221

GnomAD4 exome

AF:

0.231

AC:

336772

AN:

1460624

Hom.:

40297

Cov.:

AF XY:

0.231

AC XY:

168032

AN XY:

726654

show subpopulations

Gnomad4 AFR exome

AF:

0.112

Gnomad4 AMR exome

AF:

0.347

Gnomad4 ASJ exome

AF:

0.164

Gnomad4 EAS exome

AF:

0.300

Gnomad4 SAS exome

AF:

0.258

Gnomad4 FIN exome

AF:

0.140

Gnomad4 NFE exome

AF:

0.232

Gnomad4 OTH exome

AF:

0.214

GnomAD4 genome

AF:

0.197

AC:

29947

AN:

152034

Hom.:

3288

Cov.:

AF XY:

0.198

AC XY:

14713

AN XY:

74332

show subpopulations

Gnomad4 AFR

AF:

0.114

Gnomad4 AMR

AF:

0.292

Gnomad4 ASJ

AF:

0.169

Gnomad4 EAS

AF:

0.291

Gnomad4 SAS

AF:

0.262

Gnomad4 FIN

AF:

0.133

Gnomad4 NFE

AF:

0.224

Gnomad4 OTH

AF:

0.207

Alfa

AF:

0.220

Hom.:

9501

Bravo

AF:

0.204

TwinsUK

AF:

0.240

AC:

891

ALSPAC

AF:

0.230

AC:

888

ESP6500AA

AF:

0.118

AC:

521

ESP6500EA

AF:

0.223

AC:

1919

ExAC

AF:

0.227

AC:

27504

Asia WGS

AF:

0.284

AC:

990

AN:

3478

EpiCase

AF:

0.219

EpiControl

AF:

0.214

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.46

BayesDel_addAF

Benign

-0.38

BayesDel_noAF

Benign

-0.17

CADD

Pathogenic

DANN

Benign

0.96

DEOGEN2

Benign

0.23

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

Eigen

Pathogenic

0.70

Eigen_PC

Uncertain

0.64

FATHMM_MKL

Uncertain

0.96

LIST_S2

Benign

0.84

T;.;T;T;T;D;T;T;T;T

MetaRNN

Benign

0.0027

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

MetaSVM

Benign

-1.1

MutationAssessor

Pathogenic

3.1

.;M;.;M;.;.;.;.;.;.

MutationTaster

Benign

5.3e-9

P;P;P

PrimateAI

Uncertain

0.72

PROVEAN

Uncertain

-4.3

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

REVEL

Uncertain

0.44

Sift

Uncertain

0.0070

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

Sift4G

Uncertain

0.0040

D;D;D;D;D;D;D;D;D;D

Polyphen

0.54

.;P;.;P;.;.;.;.;.;.

Vest4

0.31, 0.31, 0.64

MPC

0.47

ClinPred

0.032

GERP RS

5.6

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.79

gMVP

0.90

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