Variant rs11151964 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.16G>A(p.Gly6Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 1,613,434 control chromosomes in the GnomAD database, including 11,681 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict 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 0.13 ( 1306 hom., cov: 32)

Exomes 𝑓: 0.12 ( 10375 hom. )

Consequence

CNDP1
NM_032649.6 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.123

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 (MetaRNN=0.0014539361).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.152 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.16G>A	p.Gly6Arg	missense_variant	1/12	ENST00000358821.8	NP_116038.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
CNDP1	ENST00000358821.8 linkuse as main transcript	c.16G>A	p.Gly6Arg	missense_variant	1/12	1	NM_032649.6	ENSP00000351682	P1
CNDP1	ENST00000582365.1 linkuse as main transcript	c.16G>A	p.Gly6Arg	missense_variant	1/11	5		ENSP00000462096
CNDP1	ENST00000585136.1 linkuse as main transcript	n.181G>A		non_coding_transcript_exon_variant	1/5	3

Frequencies

GnomAD3 genomes

AF:

0.127

AC:

19315

AN:

151980

Hom.:

1298

Cov.:

show subpopulations

Gnomad AFR

AF:

0.155

Gnomad AMI

AF:

0.218

Gnomad AMR

AF:

0.0950

Gnomad ASJ

AF:

0.212

Gnomad EAS

AF:

0.0983

Gnomad SAS

AF:

0.0868

Gnomad FIN

AF:

0.118

Gnomad MID

AF:

0.165

Gnomad NFE

AF:

0.118

Gnomad OTH

AF:

0.134

GnomAD3 exomes

AF:

0.112

AC:

28238

AN:

251258

Hom.:

1671

AF XY:

0.112

AC XY:

15275

AN XY:

135798

show subpopulations

Gnomad AFR exome

AF:

0.152

Gnomad AMR exome

AF:

0.0710

Gnomad ASJ exome

AF:

0.184

Gnomad EAS exome

AF:

0.105

Gnomad SAS exome

AF:

0.0856

Gnomad FIN exome

AF:

0.116

Gnomad NFE exome

AF:

0.120

Gnomad OTH exome

AF:

0.126

GnomAD4 exome

AF:

0.118

AC:

171985

AN:

1461336

Hom.:

10375

Cov.:

AF XY:

0.117

AC XY:

85206

AN XY:

726980

show subpopulations

Gnomad4 AFR exome

AF:

0.155

Gnomad4 AMR exome

AF:

0.0743

Gnomad4 ASJ exome

AF:

0.187

Gnomad4 EAS exome

AF:

0.0868

Gnomad4 SAS exome

AF:

0.0877

Gnomad4 FIN exome

AF:

0.120

Gnomad4 NFE exome

AF:

0.119

Gnomad4 OTH exome

AF:

0.127

GnomAD4 genome

AF:

0.127

AC:

19358

AN:

152098

Hom.:

1306

Cov.:

AF XY:

0.127

AC XY:

9445

AN XY:

74364

show subpopulations

Gnomad4 AFR

AF:

0.156

Gnomad4 AMR

AF:

0.0948

Gnomad4 ASJ

AF:

0.212

Gnomad4 EAS

AF:

0.0984

Gnomad4 SAS

AF:

0.0879

Gnomad4 FIN

AF:

0.118

Gnomad4 NFE

AF:

0.118

Gnomad4 OTH

AF:

0.134

Alfa

AF:

0.121

Hom.:

2875

Bravo

AF:

0.127

TwinsUK

AF:

0.126

AC:

469

ALSPAC

AF:

0.120

AC:

463

ESP6500AA

AF:

0.145

AC:

639

ESP6500EA

AF:

0.121

AC:

1041

ExAC

AF:

0.113

AC:

13679

Asia WGS

AF:

0.0800

AC:

276

AN:

3478

EpiCase

AF:

0.123

EpiControl

AF:

0.127

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.18

BayesDel_addAF

Benign

-0.80

BayesDel_noAF

Benign

-0.78

CADD

Benign

5.7

DANN

Benign

0.69

DEOGEN2

Benign

0.0048

.;T

Eigen

Benign

-1.4

Eigen_PC

Benign

-1.5

FATHMM_MKL

Benign

0.012

LIST_S2

Benign

0.42

.;T

MetaRNN

Benign

0.0015

T;T

MetaSVM

Benign

-0.95

MutationTaster

Benign

1.0

P;P

PrimateAI

Uncertain

0.54

PROVEAN

Benign

-0.19

N;.

REVEL

Benign

0.035

Sift

Uncertain

0.0090

D;.

Sift4G

Benign

0.071

T;D

Vest4

0.12

MutPred

0.13

Gain of MoRF binding (P = 0.0024);Gain of MoRF binding (P = 0.0024);

MPC

0.18

ClinPred

0.0075

GERP RS

-3.2

gMVP

0.25

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over