chr10-68884359-C-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_152709.5(STOX1):c.563C>A(p.Thr188Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00221 in 1,614,098 control chromosomes in the GnomAD database, including 70 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.011 ( 35 hom., cov: 32)
Exomes 𝑓: 0.0013 ( 35 hom. )
Consequence
STOX1
NM_152709.5 missense
NM_152709.5 missense
Scores
7
7
3
Clinical Significance
Conservation
PhyloP100: 7.83
Genes affected
STOX1 (HGNC:23508): (storkhead box 1) Enables RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Involved in several processes, including positive regulation of G2/M transition of mitotic cell cycle; positive regulation of protein phosphorylation; and regulation of gene expression. Located in centrosome; cytosol; and nuclear lumen. Implicated in pre-eclampsia. Biomarker of Alzheimer's disease. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.014918834).
BP6
?
Variant 10-68884359-C-A is Benign according to our data. Variant chr10-68884359-C-A is described in ClinVar as [Benign]. Clinvar id is 717159.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0112 (1707/152318) while in subpopulation AFR AF= 0.0383 (1592/41568). AF 95% confidence interval is 0.0367. There are 35 homozygotes in gnomad4. There are 838 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 35 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STOX1 | NM_152709.5 | c.563C>A | p.Thr188Asn | missense_variant | 3/4 | ENST00000298596.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STOX1 | ENST00000298596.11 | c.563C>A | p.Thr188Asn | missense_variant | 3/4 | 1 | NM_152709.5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0112 AC: 1704AN: 152200Hom.: 35 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00303 AC: 755AN: 249126Hom.: 15 AF XY: 0.00229 AC XY: 310AN XY: 135196
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GnomAD4 exome AF: 0.00128 AC: 1865AN: 1461780Hom.: 35 Cov.: 32 AF XY: 0.00111 AC XY: 808AN XY: 727186
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GnomAD4 genome ? AF: 0.0112 AC: 1707AN: 152318Hom.: 35 Cov.: 32 AF XY: 0.0113 AC XY: 838AN XY: 74480
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ESP6500AA
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 09, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
Cadd
Pathogenic
Dann
Uncertain
DEOGEN2
Uncertain
D;D;.;.
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
MetaRNN
Benign
T;T;T;T
MetaSVM
Uncertain
T
MutationAssessor
Pathogenic
M;M;.;M
MutationTaster
Benign
D;D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;D;.;D
REVEL
Uncertain
Sift
Pathogenic
D;D;.;D
Sift4G
Pathogenic
D;D;.;D
Polyphen
D;D;.;D
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
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