18-74561932-C-G

Variant summary

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

The ENST00000358821.8(CNDP1):​c.467-115C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 793,004 control chromosomes in the GnomAD database, including 21,448 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 0.24 ( 4618 hom., cov: 33)
Exomes 𝑓: 0.22 ( 16830 hom. )

Consequence

CNDP1
ENST00000358821.8 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.333
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]

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=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CNDP1NM_032649.6 linkuse as main transcriptc.467-115C>G intron_variant ENST00000358821.8 NP_116038.4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CNDP1ENST00000358821.8 linkuse as main transcriptc.467-115C>G intron_variant 1 NM_032649.6 ENSP00000351682 P1
ENST00000583702.1 linkuse as main transcriptn.104+65G>C intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.238
AC:
36147
AN:
152014
Hom.:
4612
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.313
Gnomad AMI
AF:
0.150
Gnomad AMR
AF:
0.173
Gnomad ASJ
AF:
0.228
Gnomad EAS
AF:
0.0678
Gnomad SAS
AF:
0.285
Gnomad FIN
AF:
0.170
Gnomad MID
AF:
0.285
Gnomad NFE
AF:
0.228
Gnomad OTH
AF:
0.230
GnomAD4 exome
AF:
0.222
AC:
142233
AN:
640870
Hom.:
16830
AF XY:
0.224
AC XY:
75516
AN XY:
336628
show subpopulations
Gnomad4 AFR exome
AF:
0.320
Gnomad4 AMR exome
AF:
0.137
Gnomad4 ASJ exome
AF:
0.233
Gnomad4 EAS exome
AF:
0.0620
Gnomad4 SAS exome
AF:
0.270
Gnomad4 FIN exome
AF:
0.177
Gnomad4 NFE exome
AF:
0.233
Gnomad4 OTH exome
AF:
0.230
GnomAD4 genome
AF:
0.238
AC:
36156
AN:
152134
Hom.:
4618
Cov.:
33
AF XY:
0.233
AC XY:
17315
AN XY:
74382
show subpopulations
Gnomad4 AFR
AF:
0.313
Gnomad4 AMR
AF:
0.173
Gnomad4 ASJ
AF:
0.228
Gnomad4 EAS
AF:
0.0673
Gnomad4 SAS
AF:
0.284
Gnomad4 FIN
AF:
0.170
Gnomad4 NFE
AF:
0.228
Gnomad4 OTH
AF:
0.227
Alfa
AF:
0.229
Hom.:
500
Bravo
AF:
0.240
Asia WGS
AF:
0.158
AC:
551
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
1.7
DANN
Benign
0.54

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: rs9319909; hg19: chr18-72229167; API