ENST00000261415.12:c.*9+5200dupA
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The ENST00000261415.12(CERT1):c.*9+5200dupA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00795 in 324,058 control chromosomes in the GnomAD database, including 3 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0034 ( 1 hom., cov: 31)
Exomes 𝑓: 0.011 ( 2 hom. )
Consequence
CERT1
ENST00000261415.12 intron
ENST00000261415.12 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.786
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 Likely_benign. Variant got -6 ACMG points.
BP6
Variant 5-75374136-C-CT is Benign according to our data. Variant chr5-75374136-C-CT is described in ClinVar as [Likely_benign]. Clinvar id is 2673015.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 467 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CERT1 | NM_001379004.1 | c.1724dupA | p.Leu576AlafsTer26 | frameshift_variant | Exon 16 of 16 | NP_001365933.1 | ||
CERT1 | XM_011543090.4 | c.1802dupA | p.Leu602AlafsTer26 | frameshift_variant | Exon 17 of 17 | XP_011541392.1 | ||
CERT1 | NM_001130105.1 | c.*64dupA | 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+5200dupA | intron_variant | Intron 17 of 17 | 1 | ENSP00000261415.8 | ||||
CERT1 | ENST00000642556.1 | c.1724dupA | p.Leu576AlafsTer26 | frameshift_variant | Exon 16 of 16 | ENSP00000496016.1 | ||||
CERT1 | ENST00000644072 | c.*64dupA | 3_prime_UTR_variant | Exon 18 of 18 | ENSP00000494110.2 |
Frequencies
GnomAD3 genomes AF: 0.00337 AC: 466AN: 138444Hom.: 1 Cov.: 31
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GnomAD4 exome AF: 0.0114 AC: 2108AN: 185576Hom.: 2 Cov.: 0 AF XY: 0.0113 AC XY: 1068AN XY: 94444
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GnomAD4 genome AF: 0.00337 AC: 467AN: 138482Hom.: 1 Cov.: 31 AF XY: 0.00348 AC XY: 232AN XY: 66638
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Apr 01, 2024
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
CERT1: BS1 -
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at