chr19-16831631-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PP2BP4_StrongBP6_ModerateBS2
The NM_001297595.2(SIN3B):c.365C>T(p.Ser122Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00162 in 1,613,928 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0012 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0017 ( 4 hom. )
Consequence
SIN3B
NM_001297595.2 missense
NM_001297595.2 missense
Scores
1
5
12
Clinical Significance
Conservation
PhyloP100: 5.67
Genes affected
SIN3B (HGNC:19354): (SIN3 transcription regulator family member B) Predicted to enable transcription corepressor activity. Predicted to be involved in histone deacetylation; negative regulation of transcription by RNA polymerase II; and striated muscle tissue development. Predicted to be located in nucleus. Predicted to be part of Sin3 complex. Predicted to be active in chromatin. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
PP2
?
Missense variant where missense usually causes diseases, SIN3B
BP4
?
Computational evidence support a benign effect (MetaRNN=0.010037929).
BP6
?
Variant 19-16831631-C-T is Benign according to our data. Variant chr19-16831631-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3040879.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd at 176 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SIN3B | NM_001297595.2 | c.365C>T | p.Ser122Leu | missense_variant | 3/19 | ENST00000248054.10 | |
SIN3B | NM_015260.4 | c.365C>T | p.Ser122Leu | missense_variant | 3/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SIN3B | ENST00000248054.10 | c.365C>T | p.Ser122Leu | missense_variant | 3/19 | 1 | NM_001297595.2 | P1 | |
SIN3B | ENST00000379803.5 | c.365C>T | p.Ser122Leu | missense_variant | 3/20 | 1 | |||
SIN3B | ENST00000596802.5 | c.365C>T | p.Ser122Leu | missense_variant | 3/8 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00116 AC: 176AN: 152150Hom.: 0 Cov.: 31
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00121 AC: 303AN: 251440Hom.: 1 AF XY: 0.00121 AC XY: 165AN XY: 135892
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GnomAD4 exome AF: 0.00167 AC: 2445AN: 1461660Hom.: 4 Cov.: 30 AF XY: 0.00161 AC XY: 1171AN XY: 727136
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GnomAD4 genome ? AF: 0.00116 AC: 176AN: 152268Hom.: 0 Cov.: 31 AF XY: 0.00110 AC XY: 82AN XY: 74444
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
SIN3B-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 11, 2022 | 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
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M;M
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;.;N
REVEL
Benign
Sift
Uncertain
D;.;D
Sift4G
Benign
T;T;T
Polyphen
B;B;B
Vest4
MVP
MPC
0.78
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