chr15-100455871-AT-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_001378789.1(CERS3):c.999+21del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.30 ( 7182 hom., cov: 0)
Exomes 𝑓: 0.33 ( 77118 hom. )
Consequence
CERS3
NM_001378789.1 intron
NM_001378789.1 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.669
Genes affected
CERS3 (HGNC:23752): (ceramide synthase 3) This gene is a member of the ceramide synthase family of genes. The ceramide synthase enzymes regulate sphingolipid synthesis by catalyzing the formation of ceramides from sphingoid base and acyl-coA substrates. This family member is involved in the synthesis of ceramides with ultra-long-chain acyl moieties (ULC-Cers), important to the epidermis in its role in creating a protective barrier from the environment. The protein encoded by this gene has also been implicated in modification of the lipid structures required for spermatogenesis. Mutations in this gene have been associated with male fertility defects, and epidermal defects, including ichthyosis. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Aug 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 15-100455871-AT-A is Benign according to our data. Variant chr15-100455871-AT-A is described in ClinVar as [Benign]. Clinvar id is 1282233.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CERS3 | NM_001378789.1 | c.999+21del | intron_variant | ENST00000679737.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CERS3 | ENST00000679737.1 | c.999+21del | intron_variant | NM_001378789.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.302 AC: 45915AN: 151900Hom.: 7174 Cov.: 0
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GnomAD3 exomes AF: 0.317 AC: 69210AN: 217992Hom.: 11633 AF XY: 0.328 AC XY: 38970AN XY: 118954
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GnomAD4 exome AF: 0.328 AC: 458141AN: 1394822Hom.: 77118 Cov.: 0 AF XY: 0.331 AC XY: 229707AN XY: 693224
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GnomAD4 genome ? AF: 0.302 AC: 45949AN: 152018Hom.: 7182 Cov.: 0 AF XY: 0.303 AC XY: 22504AN XY: 74318
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 10, 2018 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at