chr19-16841962-G-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_001297595.2(SIN3B):c.576G>A(p.Thr192=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000685 in 1,460,750 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 31)
Exomes 𝑓: 0.0000068 ( 0 hom. )
Consequence
SIN3B
NM_001297595.2 synonymous
NM_001297595.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.21
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 -7 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.67).
BP6
?
Variant 19-16841962-G-A is Benign according to our data. Variant chr19-16841962-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3034782.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.21 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SIN3B | NM_001297595.2 | c.576G>A | p.Thr192= | synonymous_variant | 4/19 | ENST00000248054.10 | |
SIN3B | NM_015260.4 | c.576G>A | p.Thr192= | synonymous_variant | 4/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SIN3B | ENST00000248054.10 | c.576G>A | p.Thr192= | synonymous_variant | 4/19 | 1 | NM_001297595.2 | P1 | |
SIN3B | ENST00000379803.5 | c.576G>A | p.Thr192= | synonymous_variant | 4/20 | 1 | |||
SIN3B | ENST00000596802.5 | c.576G>A | p.Thr192= | synonymous_variant | 4/8 | 1 | |||
SIN3B | ENST00000596638.1 | c.12G>A | p.Thr4= | synonymous_variant | 1/7 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD3 genomes
?
Cov.:
31
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 250260Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135510
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GnomAD4 exome AF: 0.00000685 AC: 10AN: 1460750Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7AN XY: 726726
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GnomAD4 genome ? Cov.: 31
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31
Bravo
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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 | Jul 30, 2019 | 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
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Name
Calibrated prediction
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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