rs4831732
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001413670.1(TUSC3):c.78+89056C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.953 in 152,200 control chromosomes in the GnomAD database, including 69,470 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 0.95 ( 69470 hom., cov: 32)
Consequence
TUSC3
NM_001413670.1 intron
NM_001413670.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.588
Genes affected
TUSC3 (HGNC:30242): (tumor suppressor candidate 3) This gene encodes a protein that has been associated with several biological functions including cellular magnesium uptake, protein glycosylation and embryonic development. This protein localizes to the endoplasmic reticulum and acts as a component of the oligosaccharyl transferase complex which is responsible for N-linked protein glycosylation. This gene is a candidate tumor suppressor gene. Homozygous mutations in this gene are associated with autosomal recessive nonsyndromic mental retardation-7 and in the proliferation and invasiveness of several cancers including metastatic pancreatic cancer, ovarian cancer and glioblastoma multiform. [provided by RefSeq, Oct 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=-1.02).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.992 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TUSC3 | NM_001413670.1 | c.78+89056C>A | intron_variant | NP_001400599.1 | ||||
TUSC3 | NM_001413671.1 | c.-31+94671C>A | intron_variant | NP_001400600.1 | ||||
TUSC3 | NM_001413669.1 | c.-31+94671C>A | intron_variant | NP_001400598.1 | ||||
TUSC3 | NM_001413672.1 | c.-31+28493C>A | intron_variant | NP_001400601.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TUSC3 | ENST00000503191.5 | n.189+28493C>A | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.953 AC: 144896AN: 152082Hom.: 69418 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.953 AC: 145009AN: 152200Hom.: 69470 Cov.: 32 AF XY: 0.954 AC XY: 71029AN XY: 74428
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at