ENST00000261415.12:c.*9+5197_*9+5200delAAAA
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The ENST00000261415.12(CERT1):c.*9+5197_*9+5200delAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000482 in 207,516 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: 31)
Exomes 𝑓: 0.0000048 ( 0 hom. )
Consequence
CERT1
ENST00000261415.12 intron
ENST00000261415.12 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.33
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 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 |
---|---|---|---|---|---|---|---|---|
CERT1 | NM_001379004.1 | c.1721_1724delAAAA | p.Lys574SerfsTer2 | frameshift_variant | Exon 16 of 16 | NP_001365933.1 | ||
CERT1 | XM_011543090.4 | c.1799_1802delAAAA | p.Lys600SerfsTer2 | frameshift_variant | Exon 17 of 17 | XP_011541392.1 | ||
CERT1 | NM_001130105.1 | c.*61_*64delAAAA | 3_prime_UTR_variant | Exon 19 of 19 | NP_001123577.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CERT1 | ENST00000261415.12 | c.*9+5197_*9+5200delAAAA | intron_variant | Intron 17 of 17 | 1 | ENSP00000261415.8 | ||||
CERT1 | ENST00000642556.1 | c.1721_1724delAAAA | p.Lys574SerfsTer2 | frameshift_variant | Exon 16 of 16 | ENSP00000496016.1 | ||||
CERT1 | ENST00000644072 | c.*61_*64delAAAA | 3_prime_UTR_variant | Exon 18 of 18 | ENSP00000494110.2 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 genomes
Cov.:
31
GnomAD4 exome AF: 0.00000482 AC: 1AN: 207516Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 105484
GnomAD4 exome
AF:
AC:
1
AN:
207516
Hom.:
AF XY:
AC XY:
0
AN XY:
105484
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome Cov.: 31
GnomAD4 genome
Cov.:
31
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
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