5-75374198-GA-G
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BA1
The NM_001130105.1(CERT1):c.*10-8delT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 293,662 control chromosomes in the GnomAD database, including 75 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.039 ( 74 hom., cov: 29)
Exomes 𝑓: 0.22 ( 1 hom. )
Consequence
CERT1
NM_001130105.1 splice_region, intron
NM_001130105.1 splice_region, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.108
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP6
Variant 5-75374198-GA-G is Benign according to our data. Variant chr5-75374198-GA-G is described in ClinVar as [Likely_benign]. Clinvar id is 1206283.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr5-75374198-GA-G is described in Lovd as [Benign]. Variant chr5-75374198-GA-G is described in Lovd as [Likely_benign].
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0988 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CERT1 | NM_001130105.1 | c.*10-8delT | splice_region_variant, intron_variant | NP_001123577.1 | ||||
CERT1 | NM_001379002.1 | c.*9+5138delT | intron_variant | NP_001365931.1 | ||||
CERT1 | NM_005713.3 | c.*10-8delT | splice_region_variant, intron_variant | NP_005704.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CERT1 | ENST00000261415.12 | c.*9+5138delT | intron_variant | 1 | ENSP00000261415.8 | |||||
CERT1 | ENST00000405807.10 | c.*10-8delT | splice_region_variant, intron_variant | 5 | ENSP00000383996.4 | |||||
CERT1 | ENST00000644072.2 | c.*10-8delT | splice_region_variant, intron_variant | ENSP00000494110.2 |
Frequencies
GnomAD3 genomes AF: 0.0390 AC: 3296AN: 84592Hom.: 73 Cov.: 29
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GnomAD4 exome AF: 0.215 AC: 45013AN: 209050Hom.: 1 Cov.: 0 AF XY: 0.214 AC XY: 22739AN XY: 106362
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GnomAD4 genome AF: 0.0390 AC: 3296AN: 84612Hom.: 74 Cov.: 29 AF XY: 0.0405 AC XY: 1622AN XY: 40008
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
not provided Benign:1
Likely benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
Computational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at