chr1-149923950-G-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_005850.5(SF3B4):c.978C>A(p.Pro326=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00122 in 1,589,084 control chromosomes in the GnomAD database, including 35 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0015 ( 6 hom., cov: 32)
Exomes 𝑓: 0.0012 ( 29 hom. )
Consequence
SF3B4
NM_005850.5 synonymous
NM_005850.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0760
Genes affected
SF3B4 (HGNC:10771): (splicing factor 3b subunit 4) This gene encodes one of four subunits of the splicing factor 3B. The protein encoded by this gene cross-links to a region in the pre-mRNA immediately upstream of the branchpoint sequence in pre-mRNA in the prespliceosomal complex A. It also may be involved in the assembly of the B, C and E spliceosomal complexes. In addition to RNA-binding activity, this protein interacts directly and highly specifically with subunit 2 of the splicing factor 3B. This protein contains two N-terminal RNA-recognition motifs (RRMs), consistent with the observation that it binds directly to pre-mRNA. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.5).
BP6
?
Variant 1-149923950-G-T is Benign according to our data. Variant chr1-149923950-G-T is described in ClinVar as [Benign]. Clinvar id is 292475.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.076 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00145 (221/152210) while in subpopulation EAS AF= 0.0393 (203/5160). AF 95% confidence interval is 0.0349. There are 6 homozygotes in gnomad4. There are 128 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 224 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SF3B4 | NM_005850.5 | c.978C>A | p.Pro326= | synonymous_variant | 5/6 | ENST00000271628.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SF3B4 | ENST00000271628.9 | c.978C>A | p.Pro326= | synonymous_variant | 5/6 | 1 | NM_005850.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00147 AC: 224AN: 152092Hom.: 6 Cov.: 32
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GnomAD3 exomes AF: 0.00341 AC: 731AN: 214246Hom.: 13 AF XY: 0.00299 AC XY: 355AN XY: 118708
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GnomAD4 exome AF: 0.00120 AC: 1724AN: 1436874Hom.: 29 Cov.: 32 AF XY: 0.00111 AC XY: 793AN XY: 715230
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 15, 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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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at