rs10798738
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002826.5(QSOX1):c.1288+1718A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.929 in 152,252 control chromosomes in the GnomAD database, including 65,820 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 0.93 ( 65820 hom., cov: 32)
Consequence
QSOX1
NM_002826.5 intron
NM_002826.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.49
Genes affected
QSOX1 (HGNC:9756): (quiescin sulfhydryl oxidase 1) This gene encodes a protein that contains domains of thioredoxin and ERV1, members of two long-standing gene families. The gene expression is induced as fibroblasts begin to exit the proliferative cycle and enter quiescence, suggesting that this gene plays an important role in growth regulation. Two transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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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=-0.94).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.952 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
QSOX1 | NM_002826.5 | c.1288+1718A>G | intron_variant | ENST00000367602.8 | |||
QSOX1 | NM_001004128.3 | c.1288+1718A>G | intron_variant | ||||
QSOX1 | XM_047426230.1 | c.1288+1718A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
QSOX1 | ENST00000367602.8 | c.1288+1718A>G | intron_variant | 1 | NM_002826.5 | P2 | |||
QSOX1 | ENST00000367600.5 | c.1288+1718A>G | intron_variant | 1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.929 AC: 141289AN: 152134Hom.: 65779 Cov.: 32
GnomAD3 genomes
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.929 AC: 141387AN: 152252Hom.: 65820 Cov.: 32 AF XY: 0.930 AC XY: 69200AN XY: 74428
GnomAD4 genome
?
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32
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69200
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74428
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3089
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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