rs986737217

Variant summary

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

The NM_005640.3(TAF4B):​c.319C>G​(p.Pro107Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,892 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 6.8e-7 ( 0 hom. )

Consequence

TAF4B
NM_005640.3 missense

Scores

2
5
12

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.27
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]

Genome browser will be placed here

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=0.21206409).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TAF4BNM_005640.3 linkc.319C>G p.Pro107Ala 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.319C>G p.Pro107Ala missense_variant Exon 1 of 15 1 NM_005640.3 ENSP00000269142.6 Q92750-1
TAF4BENST00000578121.5 linkc.319C>G p.Pro107Ala missense_variant Exon 1 of 15 2 ENSP00000462980.1 J3KTH2
TAF4BENST00000418698.3 linkn.319C>G non_coding_transcript_exon_variant Exon 1 of 16 5 ENSP00000389365.3 Q92750-2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
6.85e-7
AC:
1
AN:
1460892
Hom.:
0
Cov.:
31
AF XY:
0.00000138
AC XY:
1
AN XY:
726750
show subpopulations
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:
0.0000166
GnomAD4 genome
Cov.:
32
Bravo
AF:
0.00000378

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Mar 06, 2023
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.319C>G (p.P107A) alteration is located in exon 1 (coding exon 1) of the TAF4B gene. This alteration results from a C to G substitution at nucleotide position 319, causing the proline (P) at amino acid position 107 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.15
BayesDel_addAF
Benign
-0.052
T
BayesDel_noAF
Benign
-0.31
CADD
Uncertain
23
DANN
Benign
0.89
DEOGEN2
Benign
0.23
T;T
Eigen
Uncertain
0.20
Eigen_PC
Uncertain
0.22
FATHMM_MKL
Benign
0.72
D
LIST_S2
Benign
0.81
T;T
M_CAP
Benign
0.018
T
MetaRNN
Benign
0.21
T;T
MetaSVM
Benign
-0.81
T
MutationAssessor
Uncertain
2.1
M;.
PrimateAI
Uncertain
0.62
T
PROVEAN
Uncertain
-2.8
D;.
REVEL
Benign
0.11
Sift
Pathogenic
0.0
D;.
Sift4G
Pathogenic
0.0
D;D
Polyphen
0.20
B;.
Vest4
0.27
MutPred
0.34
Loss of loop (P = 0.0203);Loss of loop (P = 0.0203);
MVP
0.17
MPC
1.8
ClinPred
0.96
D
GERP RS
4.7
Varity_R
0.39
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: rs986737217; hg19: chr18-23807216; API