rs8090744

Variant summary

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

The NM_018235.3(CNDP2):​c.743-51G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0313 in 1,553,184 control chromosomes in the GnomAD database, including 1,910 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 0.069 ( 782 hom., cov: 33)
Exomes 𝑓: 0.027 ( 1128 hom. )

Consequence

CNDP2
NM_018235.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.96
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]

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=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CNDP2NM_018235.3 linkuse as main transcriptc.743-51G>A intron_variant ENST00000324262.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CNDP2ENST00000324262.9 linkuse as main transcriptc.743-51G>A intron_variant 1 NM_018235.3 P1Q96KP4-1

Frequencies

GnomAD3 genomes
AF:
0.0690
AC:
10498
AN:
152188
Hom.:
780
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.188
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0325
Gnomad ASJ
AF:
0.0533
Gnomad EAS
AF:
0.000386
Gnomad SAS
AF:
0.0577
Gnomad FIN
AF:
0.0128
Gnomad MID
AF:
0.0253
Gnomad NFE
AF:
0.0220
Gnomad OTH
AF:
0.0549
GnomAD3 exomes
AF:
0.0365
AC:
6779
AN:
185968
Hom.:
356
AF XY:
0.0349
AC XY:
3494
AN XY:
99998
show subpopulations
Gnomad AFR exome
AF:
0.190
Gnomad AMR exome
AF:
0.0177
Gnomad ASJ exome
AF:
0.0555
Gnomad EAS exome
AF:
0.000633
Gnomad SAS exome
AF:
0.0600
Gnomad FIN exome
AF:
0.0139
Gnomad NFE exome
AF:
0.0220
Gnomad OTH exome
AF:
0.0325
GnomAD4 exome
AF:
0.0272
AC:
38105
AN:
1400878
Hom.:
1128
Cov.:
29
AF XY:
0.0278
AC XY:
19261
AN XY:
691946
show subpopulations
Gnomad4 AFR exome
AF:
0.192
Gnomad4 AMR exome
AF:
0.0200
Gnomad4 ASJ exome
AF:
0.0598
Gnomad4 EAS exome
AF:
0.000208
Gnomad4 SAS exome
AF:
0.0568
Gnomad4 FIN exome
AF:
0.0149
Gnomad4 NFE exome
AF:
0.0206
Gnomad4 OTH exome
AF:
0.0356
GnomAD4 genome
AF:
0.0690
AC:
10512
AN:
152306
Hom.:
782
Cov.:
33
AF XY:
0.0679
AC XY:
5056
AN XY:
74476
show subpopulations
Gnomad4 AFR
AF:
0.188
Gnomad4 AMR
AF:
0.0325
Gnomad4 ASJ
AF:
0.0533
Gnomad4 EAS
AF:
0.000387
Gnomad4 SAS
AF:
0.0577
Gnomad4 FIN
AF:
0.0128
Gnomad4 NFE
AF:
0.0220
Gnomad4 OTH
AF:
0.0539
Alfa
AF:
0.0233
Hom.:
38
Bravo
AF:
0.0758
Asia WGS
AF:
0.0270
AC:
92
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.63
DANN
Benign
0.50
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

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.

Other links and lift over

dbSNP: rs8090744; hg19: chr18-72180743; API