chr18-26227063-G-A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_005640.3(TAF4B):​c.130G>A​(p.Ala44Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

TAF4B
NM_005640.3 missense

Scores

2
17

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.798
Variant links:
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 Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.12175104).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TAF4BNM_005640.3 linkc.130G>A p.Ala44Thr missense_variant Exon 1 of 15 ENST00000269142.10 NP_005631.1 Q92750-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TAF4BENST00000269142.10 linkc.130G>A p.Ala44Thr missense_variant Exon 1 of 15 1 NM_005640.3 ENSP00000269142.6 Q92750-1
TAF4BENST00000578121.5 linkc.130G>A p.Ala44Thr missense_variant Exon 1 of 15 2 ENSP00000462980.1 J3KTH2
TAF4BENST00000418698.3 linkn.130G>A non_coding_transcript_exon_variant Exon 1 of 16 5 ENSP00000389365.3 Q92750-2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1443048
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
718124
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.086
BayesDel_addAF
Benign
-0.17
T
BayesDel_noAF
Benign
-0.48
CADD
Benign
20
DANN
Benign
0.96
DEOGEN2
Benign
0.055
T;T
Eigen
Benign
-0.33
Eigen_PC
Benign
-0.25
FATHMM_MKL
Benign
0.46
N
LIST_S2
Benign
0.80
T;T
M_CAP
Benign
0.0095
T
MetaRNN
Benign
0.12
T;T
MetaSVM
Benign
-0.99
T
MutationAssessor
Benign
1.9
L;.
PrimateAI
Uncertain
0.62
T
PROVEAN
Benign
0.29
N;.
REVEL
Benign
0.021
Sift
Uncertain
0.013
D;.
Sift4G
Benign
0.25
T;T
Polyphen
0.80
P;.
Vest4
0.14
MutPred
0.33
Gain of phosphorylation at A44 (P = 0.0485);Gain of phosphorylation at A44 (P = 0.0485);
MVP
0.15
MPC
1.3
ClinPred
0.75
D
GERP RS
1.5
Varity_R
0.052
gMVP
0.32

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
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: rs78262333; hg19: chr18-23807027; API