chr15-100456190-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001378789.1(CERS3):c.846-144C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.994 in 487,918 control chromosomes in the GnomAD database, including 241,065 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.98 ( 73880 hom., cov: 33)
Exomes 𝑓: 1.0 ( 167185 hom. )
Consequence
CERS3
NM_001378789.1 intron
NM_001378789.1 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.264
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
?
Variant 15-100456190-G-A is Benign according to our data. Variant chr15-100456190-G-A is described in ClinVar as [Benign]. Clinvar id is 1288997.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.994 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CERS3 | NM_001378789.1 | c.846-144C>T | intron_variant | ENST00000679737.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CERS3 | ENST00000679737.1 | c.846-144C>T | intron_variant | NM_001378789.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.985 AC: 149873AN: 152196Hom.: 73825 Cov.: 33
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GnomAD4 exome AF: 0.998 AC: 334968AN: 335606Hom.: 167185 AF XY: 0.998 AC XY: 173186AN XY: 173468
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GnomAD4 genome ? AF: 0.985 AC: 149987AN: 152312Hom.: 73880 Cov.: 33 AF XY: 0.986 AC XY: 73400AN XY: 74474
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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 | Jun 18, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at