Genetic Variant TAF11:c.*918A>C (chr6-34877672-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005643.4(TAF11):c.*918A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 152,144 control chromosomes in the GnomAD database, including 20,791 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.46 ( 20778 hom., cov: 31)

Exomes 𝑓: 0.22 ( 13 hom. )

Consequence

TAF11
NM_005643.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.454

Publications

30 publications found

Variant links:

Genes affected

TAF11 (HGNC:11544): (TATA-box binding protein associated factor 11) Initiation of transcription by RNA polymerase II requires the activities of more than 70 polypeptides. The protein that coordinates these activities is transcription factor IID (TFIID), which binds to the core promoter to position the polymerase properly, serves as the scaffold for assembly of the remainder of the transcription complex, and acts as a channel for regulatory signals. TFIID is composed of the TATA-binding protein (TBP) and a group of evolutionarily conserved proteins known as TBP-associated factors or TAFs. TAFs may participate in basal transcription, serve as coactivators, function in promoter recognition or modify general transcription factors (GTFs) to facilitate complex assembly and transcription initiation. This gene encodes a small subunit of TFIID that is present in all TFIID complexes and interacts with TBP. This subunit also interacts with another small subunit, TAF13, to form a heterodimer with a structure similar to the histone core structure. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2012]

TAF11 links:

BLTP3A (HGNC:21216): (bridge-like lipid transfer protein family member 3A) Enables histone deacetylase binding activity and identical protein binding activity. [provided by Alliance of Genome Resources, Apr 2022]

BLTP3A links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAF11	NM_005643.4 link	c.*918A>C		3_prime_UTR_variant	Exon 5 of 5	ENST00000361288.9	NP_005634.1
BLTP3A	NM_017754.4 link	c.*5234T>G		downstream_gene_variant		ENST00000192788.6	NP_060224.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAF11	ENST00000361288.9 link	c.*918A>C		3_prime_UTR_variant	Exon 5 of 5	1	NM_005643.4	ENSP00000354633.4
BLTP3A	ENST00000192788.6 link	c.*5234T>G		downstream_gene_variant		1	NM_017754.4	ENSP00000192788.5

Frequencies

GnomAD3 genomes

AF:

0.457

AC:

69367

AN:

151678

Hom.:

20721

Cov.:

show subpopulations

Gnomad AFR

AF:

0.831

Gnomad AMI

AF:

0.148

Gnomad AMR

AF:

0.393

Gnomad ASJ

AF:

0.482

Gnomad EAS

AF:

0.696

Gnomad SAS

AF:

0.422

Gnomad FIN

AF:

0.211

Gnomad MID

AF:

0.465

Gnomad NFE

AF:

0.269

Gnomad OTH

AF:

0.491

GnomAD4 exome

AF:

0.216

AC:

AN:

348

Hom.:

Cov.:

AF XY:

0.226

AC XY:

AN XY:

212

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.213

AC:

AN:

342

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

AN:

Other (OTH)

AF:

0.250

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.516

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.458

AC:

69471

AN:

151796

Hom.:

20778

Cov.:

AF XY:

0.457

AC XY:

33868

AN XY:

74162

show subpopulations

African (AFR)

AF:

0.831

AC:

34383

AN:

41370

American (AMR)

AF:

0.392

AC:

5973

AN:

15222

Ashkenazi Jewish (ASJ)

AF:

0.482

AC:

1671

AN:

3470

East Asian (EAS)

AF:

0.696

AC:

3577

AN:

5142

South Asian (SAS)

AF:

0.423

AC:

2027

AN:

4794

European-Finnish (FIN)

AF:

0.211

AC:

2223

AN:

10532

Middle Eastern (MID)

AF:

0.462

AC:

134

AN:

290

European-Non Finnish (NFE)

AF:

0.269

AC:

18312

AN:

67952

Other (OTH)

AF:

0.491

AC:

1036

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1409

2818

4228

5637

7046

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

580

1160

1740

2320

2900

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.341

Hom.:

33763

Bravo

AF:

0.492

Asia WGS

AF:

0.546

AC:

1899

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

4.1

(source)

DANN

Benign

0.66

PhyloP100

0.45

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over