GeneBe

chr10-122836358-GAAAAAAA-G

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_022034.6(CUZD1):​c.818-15_818-9delTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000375 in 1,067,802 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)
Exomes 𝑓: 0.0000037 ( 0 hom. )

Consequence

CUZD1
NM_022034.6 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.31

Publications

0 publications found
Variant links:
Genes affected
CUZD1 (HGNC:17937): (CUB and zona pellucida like domains 1) Predicted to be involved in trypsinogen activation. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]
CUZD1 Gene-Disease associations (from GenCC):
  • schizophrenia
    Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CUZD1NM_022034.6 linkc.818-15_818-9delTTTTTTT intron_variant Intron 5 of 8 ENST00000392790.6 NP_071317.2 Q86UP6-1
CUZD1NR_037912.2 linkn.681-15_681-9delTTTTTTT intron_variant Intron 4 of 7
FAM24B-CUZD1NR_037915.1 linkn.1494-15_1494-9delTTTTTTT intron_variant Intron 7 of 10

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CUZD1ENST00000392790.6 linkc.818-15_818-9delTTTTTTT intron_variant Intron 5 of 8 1 NM_022034.6 ENSP00000376540.1 Q86UP6-1
ENSG00000286088ENST00000368904.6 linkn.818-15_818-9delTTTTTTT intron_variant Intron 6 of 9 1 ENSP00000357900.2 A0A499FIG0

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
0.00000375
AC:
4
AN:
1067802
Hom.:
0
AF XY:
0.00000764
AC XY:
4
AN XY:
523684
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
0.00
AC:
0
AN:
22126
American (AMR)
AF:
0.00
AC:
0
AN:
16390
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
16704
East Asian (EAS)
AF:
0.00
AC:
0
AN:
29120
South Asian (SAS)
AF:
0.00
AC:
0
AN:
46782
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
33656
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
3634
European-Non Finnish (NFE)
AF:
0.00000468
AC:
4
AN:
854962
Other (OTH)
AF:
0.00
AC:
0
AN:
44428
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.250
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Cov.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
1.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs11365591; hg19: chr10-124595874; API