15-75372063-G-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBS1BS2
The NM_001145358.2(SIN3A):c.3738C>T(p.Thr1246=) variant causes a synonymous change. The variant allele was found at a frequency of 0.0000489 in 1,614,156 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: 𝑓 0.00020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000033 ( 0 hom. )
Consequence
SIN3A
NM_001145358.2 synonymous
NM_001145358.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.98
Genes affected
SIN3A (HGNC:19353): (SIN3 transcription regulator family member A) The protein encoded by this gene is a transcriptional regulatory protein. It contains paired amphipathic helix (PAH) domains, which are important for protein-protein interactions and may mediate repression by the Mad-Max complex. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.41).
BP6
?
Variant 15-75372063-G-A is Benign according to our data. Variant chr15-75372063-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2159914.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000204 (31/152262) while in subpopulation AFR AF= 0.000746 (31/41528). AF 95% confidence interval is 0.000539. There are 0 homozygotes in gnomad4. There are 17 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 25 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SIN3A | NM_001145358.2 | c.3738C>T | p.Thr1246= | synonymous_variant | 21/21 | ENST00000394947.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SIN3A | ENST00000394947.8 | c.3738C>T | p.Thr1246= | synonymous_variant | 21/21 | 1 | NM_001145358.2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000164 AC: 25AN: 152144Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000437 AC: 11AN: 251492Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135922
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GnomAD4 exome AF: 0.0000328 AC: 48AN: 1461894Hom.: 0 Cov.: 31 AF XY: 0.0000344 AC XY: 25AN XY: 727248
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 06, 2023 | - - |
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