ENST00000261415.12:c.*9+5135_*9+5138delTTTT
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.
The ENST00000261415.12(CERT1):c.*9+5135_*9+5138delTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00652 in 296,762 control chromosomes in the GnomAD database, with no homozygous occurrence. There is a variant allele frequency bias in the population database for this variant (GnomAdExome4), which may indicate mosaicism or somatic mutations in the reference population data. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000012 ( 0 hom., cov: 29)
Exomes 𝑓: 0.0091 ( 0 hom. )
Consequence
CERT1
ENST00000261415.12 intron
ENST00000261415.12 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.131
Publications
0 publications found
Genes affected
CERT1 (HGNC:2205): (ceramide transporter 1) This gene encodes a kinase that specifically phosphorylates the N-terminal region of the non-collagenous domain of the alpha 3 chain of type IV collagen, known as the Goodpasture antigen. Goodpasture disease is the result of an autoimmune response directed at this antigen. One isoform of this protein is also involved in ceramide intracellular transport. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
CERT1 Gene-Disease associations (from GenCC):
- intellectual disability, autosomal dominant 34Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Variant Effect in Transcripts
ACMG analysis was done for transcript: ENST00000261415.12. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| CERT1 | NM_001130105.1 | c.*10-11_*10-8delTTTT | splice_region intron | N/A | NP_001123577.1 | Q9Y5P4-3 | |||
| CERT1 | NM_001379002.1 | c.*9+5135_*9+5138delTTTT | intron | N/A | NP_001365931.1 | Q9Y5P4-1 | |||
| CERT1 | NM_005713.3 | c.*10-11_*10-8delTTTT | splice_region intron | N/A | NP_005704.1 | Q9Y5P4-1 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| CERT1 | ENST00000261415.12 | TSL:1 | c.*9+5135_*9+5138delTTTT | intron | N/A | ENSP00000261415.8 | Q9Y5P4-1 | ||
| CERT1 | ENST00000405807.10 | TSL:5 | c.*10-11_*10-8delTTTT | splice_region intron | N/A | ENSP00000383996.4 | Q9Y5P4-3 | ||
| CERT1 | ENST00000957920.1 | c.*10-11_*10-8delTTTT | splice_region intron | N/A | ENSP00000627979.1 |
Frequencies
GnomAD3 genomes 0.0000118 AC: 1AN: 84602Hom.: 0 Cov.: 29 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
84602
Hom.:
Cov.:
29
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.00911 AC: 1933AN: 212160Hom.: 0 AF XY: 0.00887 AC XY: 957AN XY: 107944 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
1933
AN:
212160
Hom.:
AF XY:
AC XY:
957
AN XY:
107944
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
62
AN:
6154
American (AMR)
AF:
AC:
62
AN:
6408
Ashkenazi Jewish (ASJ)
AF:
AC:
68
AN:
7992
East Asian (EAS)
AF:
AC:
172
AN:
20050
South Asian (SAS)
AF:
AC:
25
AN:
2410
European-Finnish (FIN)
AF:
AC:
159
AN:
16604
Middle Eastern (MID)
AF:
AC:
13
AN:
1114
European-Non Finnish (NFE)
AF:
AC:
1220
AN:
137364
Other (OTH)
AF:
AC:
152
AN:
14064
⚠️ 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: 0.254
Heterozygous variant carriers
0
248
497
745
994
1242
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
10
20
30
40
50
<30
30-35
35-40
40-45
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>80
Age
GnomAD4 genome 0.0000118 AC: 1AN: 84602Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 39976 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
84602
Hom.:
Cov.:
29
AF XY:
AC XY:
0
AN XY:
39976
show subpopulations
African (AFR)
AF:
AC:
0
AN:
24480
American (AMR)
AF:
AC:
0
AN:
7248
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
2136
East Asian (EAS)
AF:
AC:
0
AN:
3096
South Asian (SAS)
AF:
AC:
0
AN:
2658
European-Finnish (FIN)
AF:
AC:
0
AN:
3708
Middle Eastern (MID)
AF:
AC:
0
AN:
136
European-Non Finnish (NFE)
AF:
AC:
1
AN:
39538
Other (OTH)
AF:
AC:
0
AN:
1096
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
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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