chr18-26267611-T-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_005640.3(TAF4B):c.585T>G(p.Pro195=) variant causes a synonymous change. The variant allele was found at a frequency of 0.000185 in 1,613,344 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00019 ( 1 hom. )
Consequence
TAF4B
NM_005640.3 synonymous
NM_005640.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 4.43
Genes affected
TAF4B (HGNC:11538): (TATA-box binding protein associated factor 4b) TATA binding protein (TBP) and TBP-associated factors (TAFs) participate in the formation of the TFIID protein complex, which is involved in initiation of transcription of genes by RNA polymerase II. This gene encodes a cell type-specific TAF that may be responsible for mediating transcription by a subset of activators in B cells. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jun 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.52).
BP6
?
Variant 18-26267611-T-G is Benign according to our data. Variant chr18-26267611-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 748624.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TAF4B | NM_005640.3 | c.585T>G | p.Pro195= | synonymous_variant | 3/15 | ENST00000269142.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TAF4B | ENST00000269142.10 | c.585T>G | p.Pro195= | synonymous_variant | 3/15 | 1 | NM_005640.3 | P4 | |
TAF4B | ENST00000578121.5 | c.585T>G | p.Pro195= | synonymous_variant | 3/15 | 2 | A2 | ||
TAF4B | ENST00000418698.3 | c.585T>G | p.Pro195= | synonymous_variant, NMD_transcript_variant | 3/16 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000131 AC: 20AN: 152240Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000353 AC: 88AN: 249478Hom.: 0 AF XY: 0.000325 AC XY: 44AN XY: 135350
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GnomAD4 exome AF: 0.000190 AC: 278AN: 1460986Hom.: 1 Cov.: 29 AF XY: 0.000193 AC XY: 140AN XY: 726842
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
TAF4B-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 22, 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). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 23, 2018 | - - |
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
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