11-66055135-G-C
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Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_006842.3(SF3B2):āc.318G>Cā(p.Pro106=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.00012 ( 0 hom., cov: 32)
Exomes š: 0.00022 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
SF3B2
NM_006842.3 synonymous
NM_006842.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.29
Genes affected
SF3B2 (HGNC:10769): (splicing factor 3b subunit 2) This gene encodes subunit 2 of the splicing factor 3b protein complex. Splicing factor 3b, together with splicing factor 3a and a 12S RNA unit, forms the U2 small nuclear ribonucleoproteins complex (U2 snRNP). The splicing factor 3b/3a complex binds pre-mRNA upstream of the intron's branch site in a sequence-independent manner and may anchor the U2 snRNP to the pre-mRNA. Splicing factor 3b is also a component of the minor U12-type spliceosome. Subunit 2 associates with pre-mRNA upstream of the branch site at the anchoring site. Subunit 2 also interacts directly with subunit 4 of the splicing factor 3b complex. Subunit 2 is a highly hydrophilic protein with a proline-rich N-terminus and a glutamate-rich stretch in the C-terminus. [provided by RefSeq, Jul 2008]
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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=-0.88).
BP6
?
Variant 11-66055135-G-C is Benign according to our data. Variant chr11-66055135-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 2578660.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-2.29 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SF3B2 | NM_006842.3 | c.318G>C | p.Pro106= | synonymous_variant | 4/22 | ENST00000322535.11 | |
SF3B2 | XM_005273726.5 | c.318G>C | p.Pro106= | synonymous_variant | 4/22 | ||
SF3B2 | XM_011544740.4 | c.318G>C | p.Pro106= | synonymous_variant | 4/22 | ||
SF3B2 | XM_017017144.3 | c.318G>C | p.Pro106= | synonymous_variant | 4/22 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SF3B2 | ENST00000322535.11 | c.318G>C | p.Pro106= | synonymous_variant | 4/22 | 1 | NM_006842.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 17AN: 144190Hom.: 0 Cov.: 32 FAILED QC
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000221 AC: 237AN: 1070404Hom.: 0 Cov.: 32 AF XY: 0.000228 AC XY: 121AN XY: 530134
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GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.000118 AC: 17AN: 144332Hom.: 0 Cov.: 32 AF XY: 0.0000711 AC XY: 5AN XY: 70300
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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 | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2023 | SF3B2: BP4, BP7 - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at