GeneBe

rs33990520

Variant names:

Variant summary

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

The NM_024913.5(CPED1):​c.750-9_750-3delTTTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000742 in 1,346,868 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: 7.4e-7 ( 0 hom. )

Consequence

CPED1
NM_024913.5 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.48

Publications

0 publications found
Variant links:
Genes affected
CPED1 (HGNC:26159): (cadherin like and PC-esterase domain containing 1) Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

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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
CPED1NM_024913.5 linkc.750-9_750-3delTTTTTTT splice_region_variant, intron_variant Intron 6 of 22 ENST00000310396.10 NP_079189.4 A4D0V7-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CPED1ENST00000310396.10 linkc.750-17_750-11delTTTTTTT intron_variant Intron 6 of 22 1 NM_024913.5 ENSP00000309772.5 A4D0V7-1

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
7.42e-7
AC:
1
AN:
1346868
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
671652
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
29856
American (AMR)
AF:
0.00
AC:
0
AN:
37658
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
24014
East Asian (EAS)
AF:
0.00
AC:
0
AN:
37084
South Asian (SAS)
AF:
0.00
AC:
0
AN:
79552
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
46908
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5398
European-Non Finnish (NFE)
AF:
9.70e-7
AC:
1
AN:
1030698
Other (OTH)
AF:
0.00
AC:
0
AN:
55700
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
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
1.5

Splicing

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

Publications

Other links and lift over

dbSNP: rs33990520; hg19: chr7-120739962; API