rs201319446
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_018013.4(SOBP):c.1321C>T(p.Pro441Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0025 in 1,611,196 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.0017 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0026 ( 9 hom. )
Consequence
SOBP
NM_018013.4 missense
NM_018013.4 missense
Scores
2
6
11
Clinical Significance
Conservation
PhyloP100: 7.22
Genes affected
SOBP (HGNC:29256): (sine oculis binding protein homolog) The protein encoded by this gene is a nuclear zinc finger protein that is involved in development of the cochlea. Defects in this gene have also been linked to intellectual disability. [provided by RefSeq, Mar 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.017431855).
BP6
?
Variant 6-107634165-C-T is Benign according to our data. Variant chr6-107634165-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 212276.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=1, Uncertain_significance=2}.
BS2
?
High Homozygotes in GnomAdExome4 at 9 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SOBP | NM_018013.4 | c.1321C>T | p.Pro441Ser | missense_variant | 6/7 | ENST00000317357.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SOBP | ENST00000317357.10 | c.1321C>T | p.Pro441Ser | missense_variant | 6/7 | 5 | NM_018013.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00169 AC: 257AN: 152134Hom.: 0 Cov.: 33
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?
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GnomAD3 exomes AF: 0.00123 AC: 295AN: 240592Hom.: 1 AF XY: 0.00116 AC XY: 153AN XY: 131952
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GnomAD4 exome AF: 0.00259 AC: 3779AN: 1458944Hom.: 9 Cov.: 33 AF XY: 0.00250 AC XY: 1813AN XY: 725886
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GnomAD4 genome ? AF: 0.00169 AC: 257AN: 152252Hom.: 0 Cov.: 33 AF XY: 0.00146 AC XY: 109AN XY: 74434
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ExAC
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:2Benign:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jun 25, 2014 | - - |
Intellectual disability, anterior maxillary protrusion, and strabismus Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 31, 2018 | - - |
SOBP-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 03, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D
M_CAP
Benign
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D
REVEL
Benign
Sift
Pathogenic
D
Sift4G
Benign
T
Polyphen
P
Vest4
MVP
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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