rs6109692
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6BP7BA1
The NM_018327.4(SPTLC3):c.693C>T(p.Phe231=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 1,612,992 control chromosomes in the GnomAD database, including 8,756 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars).
Frequency
Genomes: 𝑓 0.093 ( 751 hom., cov: 32)
Exomes 𝑓: 0.10 ( 8005 hom. )
Consequence
SPTLC3
NM_018327.4 synonymous
NM_018327.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.785
Genes affected
SPTLC3 (HGNC:16253): (serine palmitoyltransferase long chain base subunit 3) This gene encodes a subunit of the serine palmitoyltransferase complex which catalyzes the rate-limiting step in sphingolipid biosynthesis. This subunit metabolizes lauroyl- and myristoyl-CoA and generates C14 and C16-sphingoid bases. [provided by RefSeq, Mar 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.28).
BP6
?
Variant 20-13091168-C-T is Benign according to our data. Variant chr20-13091168-C-T is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=0.785 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPTLC3 | NM_018327.4 | c.693C>T | p.Phe231= | synonymous_variant | 5/12 | ENST00000399002.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPTLC3 | ENST00000399002.7 | c.693C>T | p.Phe231= | synonymous_variant | 5/12 | 1 | NM_018327.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0935 AC: 14221AN: 152024Hom.: 751 Cov.: 32
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GnomAD3 exomes AF: 0.0936 AC: 23333AN: 249306Hom.: 1200 AF XY: 0.0957 AC XY: 12939AN XY: 135258
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GnomAD4 exome AF: 0.103 AC: 150315AN: 1460850Hom.: 8005 Cov.: 31 AF XY: 0.103 AC XY: 74518AN XY: 726714
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GnomAD4 genome ? AF: 0.0935 AC: 14223AN: 152142Hom.: 751 Cov.: 32 AF XY: 0.0936 AC XY: 6961AN XY: 74378
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Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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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