rs5753158
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_174975.5(SEC14L3):c.*311G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 1,052,516 control chromosomes in the GnomAD database, including 39,994 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.25 ( 5017 hom., cov: 32)
Exomes 𝑓: 0.28 ( 34977 hom. )
Consequence
SEC14L3
NM_174975.5 3_prime_UTR
NM_174975.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.425
Genes affected
SEC14L3 (HGNC:18655): (SEC14 like lipid binding 3) The protein encoded by this gene is highly similar to the protein encoded by the Saccharomyces cerevisiae SEC14 gene. The SEC14 protein is a phophatidylinositol transfer protein that is essential for biogenesis of Golgi-derived transport vesicles, and thus is required for the export of yeast secretory proteins from the Golgi complex. The specific function of this protein has not yet been determined. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jul 2012]
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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=-0.81).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEC14L3 | NM_174975.5 | c.*311G>A | 3_prime_UTR_variant | 12/12 | ENST00000215812.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEC14L3 | ENST00000215812.9 | c.*311G>A | 3_prime_UTR_variant | 12/12 | 1 | NM_174975.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.255 AC: 38721AN: 152004Hom.: 5021 Cov.: 32
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GnomAD4 exome AF: 0.277 AC: 249300AN: 900394Hom.: 34977 Cov.: 30 AF XY: 0.277 AC XY: 115968AN XY: 419142
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GnomAD4 genome ? AF: 0.255 AC: 38733AN: 152122Hom.: 5017 Cov.: 32 AF XY: 0.251 AC XY: 18678AN XY: 74370
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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