18-74583526-T-C

Variant summary

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

The NM_032649.6(CNDP1):​c.1310-35T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.662 in 1,601,126 control chromosomes in the GnomAD database, including 353,701 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. There are indicators that this mutation may affect the branch point..

Frequency

Genomes: 𝑓 0.61 ( 29038 hom., cov: 31)
Exomes 𝑓: 0.67 ( 324663 hom. )

Consequence

CNDP1
NM_032649.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.40
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
This place is a probable branch point but likely benign (scored 2 / 10). Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CNDP1NM_032649.6 linkuse as main transcriptc.1310-35T>C intron_variant ENST00000358821.8 NP_116038.4 Q96KN2
LOC124904324XR_007066415.1 linkuse as main transcriptn.152A>G non_coding_transcript_exon_variant 1/2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CNDP1ENST00000358821.8 linkuse as main transcriptc.1310-35T>C intron_variant 1 NM_032649.6 ENSP00000351682.3 Q96KN2
CNDP1ENST00000582365.1 linkuse as main transcriptc.1181-35T>C intron_variant 5 ENSP00000462096.1 J3KRP0
CNDP1ENST00000582461.1 linkuse as main transcriptn.2191-35T>C intron_variant 5
CNDP1ENST00000584004.5 linkuse as main transcriptn.834-35T>C intron_variant 2

Frequencies

GnomAD3 genomes
AF:
0.609
AC:
92431
AN:
151852
Hom.:
29033
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.441
Gnomad AMI
AF:
0.647
Gnomad AMR
AF:
0.688
Gnomad ASJ
AF:
0.665
Gnomad EAS
AF:
0.646
Gnomad SAS
AF:
0.727
Gnomad FIN
AF:
0.676
Gnomad MID
AF:
0.706
Gnomad NFE
AF:
0.666
Gnomad OTH
AF:
0.643
GnomAD3 exomes
AF:
0.669
AC:
167278
AN:
250178
Hom.:
56716
AF XY:
0.674
AC XY:
91180
AN XY:
135200
show subpopulations
Gnomad AFR exome
AF:
0.437
Gnomad AMR exome
AF:
0.723
Gnomad ASJ exome
AF:
0.647
Gnomad EAS exome
AF:
0.653
Gnomad SAS exome
AF:
0.729
Gnomad FIN exome
AF:
0.687
Gnomad NFE exome
AF:
0.669
Gnomad OTH exome
AF:
0.689
GnomAD4 exome
AF:
0.667
AC:
966994
AN:
1449156
Hom.:
324663
Cov.:
27
AF XY:
0.670
AC XY:
482722
AN XY:
720992
show subpopulations
Gnomad4 AFR exome
AF:
0.432
Gnomad4 AMR exome
AF:
0.720
Gnomad4 ASJ exome
AF:
0.648
Gnomad4 EAS exome
AF:
0.654
Gnomad4 SAS exome
AF:
0.726
Gnomad4 FIN exome
AF:
0.683
Gnomad4 NFE exome
AF:
0.668
Gnomad4 OTH exome
AF:
0.659
GnomAD4 genome
AF:
0.608
AC:
92470
AN:
151970
Hom.:
29038
Cov.:
31
AF XY:
0.612
AC XY:
45446
AN XY:
74272
show subpopulations
Gnomad4 AFR
AF:
0.441
Gnomad4 AMR
AF:
0.689
Gnomad4 ASJ
AF:
0.665
Gnomad4 EAS
AF:
0.647
Gnomad4 SAS
AF:
0.726
Gnomad4 FIN
AF:
0.676
Gnomad4 NFE
AF:
0.666
Gnomad4 OTH
AF:
0.640
Alfa
AF:
0.633
Hom.:
6361
Bravo
AF:
0.605
Asia WGS
AF:
0.663
AC:
2308
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
2.6
DANN
Benign
0.45
BranchPoint Hunter
2.0

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.

Other links and lift over

dbSNP: rs11659237; hg19: chr18-72250762; COSMIC: COSV62594146; API