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GeneBe

11-66055135-G-C

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7

The NM_006842.3(SF3B2):c.318G>C(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 (★).

Frequency

Genomes: 𝑓 0.00012 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00022 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

SF3B2
NM_006842.3 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.29
Variant links:
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
SF3B2NM_006842.3 linkuse as main transcriptc.318G>C p.Pro106= synonymous_variant 4/22 ENST00000322535.11
SF3B2XM_005273726.5 linkuse as main transcriptc.318G>C p.Pro106= synonymous_variant 4/22
SF3B2XM_011544740.4 linkuse as main transcriptc.318G>C p.Pro106= synonymous_variant 4/22
SF3B2XM_017017144.3 linkuse as main transcriptc.318G>C p.Pro106= synonymous_variant 4/22

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SF3B2ENST00000322535.11 linkuse as main transcriptc.318G>C p.Pro106= synonymous_variant 4/221 NM_006842.3 P1

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
17
AN:
144190
Hom.:
0
Cov.:
32
FAILED QC
Gnomad AFR
AF:
0.0000498
Gnomad AMI
AF:
0.00116
Gnomad AMR
AF:
0.000137
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000700
Gnomad SAS
AF:
0.000999
Gnomad FIN
AF:
0.000220
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000458
Gnomad OTH
AF:
0.00
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.000221
AC:
237
AN:
1070404
Hom.:
0
Cov.:
32
AF XY:
0.000228
AC XY:
121
AN XY:
530134
show subpopulations
Gnomad4 AFR exome
AF:
0.000384
Gnomad4 AMR exome
AF:
0.000271
Gnomad4 ASJ exome
AF:
0.000734
Gnomad4 EAS exome
AF:
0.000592
Gnomad4 SAS exome
AF:
0.0000133
Gnomad4 FIN exome
AF:
0.000413
Gnomad4 NFE exome
AF:
0.000200
Gnomad4 OTH exome
AF:
0.000403
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.000118
AC:
17
AN:
144332
Hom.:
0
Cov.:
32
AF XY:
0.0000711
AC XY:
5
AN XY:
70300
show subpopulations
Gnomad4 AFR
AF:
0.0000497
Gnomad4 AMR
AF:
0.000137
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000700
Gnomad4 SAS
AF:
0.000996
Gnomad4 FIN
AF:
0.000220
Gnomad4 NFE
AF:
0.0000458
Gnomad4 OTH
AF:
0.00

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 submitterclinical testingCeGaT Center for Human Genetics TuebingenJul 01, 2023SF3B2: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
Cadd
Benign
0.61
Dann
Benign
0.56

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.10
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs756928979; hg19: chr11-65822606; API