9-136208887-G-A
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_181701.4(QSOX2):c.1938C>T(p.Gly646Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00248 in 1,613,954 control chromosomes in the GnomAD database, including 56 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0017 ( 2 hom., cov: 32)
Exomes 𝑓: 0.0026 ( 54 hom. )
Consequence
QSOX2
NM_181701.4 synonymous
NM_181701.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.182
Genes affected
QSOX2 (HGNC:30249): (quiescin sulfhydryl oxidase 2) QSOX2 is a member of the sulfhydryl oxidase/quiescin-6 (Q6) family (QSOX1; MIM 603120) that regulates the sensitization of neuroblastoma cells for IFN-gamma (IFNG; MIM 147570)-induced cell death (Wittke et al., 2003 [PubMed 14633699]).[supplied by OMIM, Jun 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
Variant 9-136208887-G-A is Benign according to our data. Variant chr9-136208887-G-A is described in ClinVar as [Benign]. Clinvar id is 771171.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.182 with no splicing effect.
BS1
Variant frequency is greater than expected in population sas. gnomad4_exome allele frequency = 0.00256 (3744/1461684) while in subpopulation SAS AF= 0.0203 (1748/86258). AF 95% confidence interval is 0.0195. There are 54 homozygotes in gnomad4_exome. There are 2282 alleles in male gnomad4_exome subpopulation. Median coverage is 30. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 2 AR gene
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00170 AC: 259AN: 152152Hom.: 2 Cov.: 32
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GnomAD3 exomes AF: 0.00402 AC: 1009AN: 251134Hom.: 13 AF XY: 0.00493 AC XY: 669AN XY: 135768
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GnomAD4 exome AF: 0.00256 AC: 3744AN: 1461684Hom.: 54 Cov.: 30 AF XY: 0.00314 AC XY: 2282AN XY: 727136
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GnomAD4 genome AF: 0.00170 AC: 259AN: 152270Hom.: 2 Cov.: 32 AF XY: 0.00219 AC XY: 163AN XY: 74438
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 03, 2018 | - - |
Computational 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
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at