rs2985

Positions:

• chr6-34877871-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005643.4(TAF11):​c.*719A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 152,142 control chromosomes in the GnomAD database, including 9,989 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 0.31 (9989 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: TAF11 NM_005643.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.766

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TAF11	NM_005643.4	c.*719A>G		3_prime_UTR_variant	5/5	ENST00000361288.9
TAF11	NM_001270488.1	c.*793A>G		3_prime_UTR_variant	4/4
TAF11	XM_011514827.3	c.*719A>G		3_prime_UTR_variant	5/5
TAF11	XM_047419270.1	c.*793A>G		3_prime_UTR_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TAF11	ENST00000361288.9	c.*719A>G		3_prime_UTR_variant	5/5	1	NM_005643.4	P1

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46722 AN: 152024 Hom.: 9969 Cov.: 32

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.319

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.307 AC: 46783 AN: 152142 Hom.: 9989 Cov.: 32 AF XY: 0.307 AC XY: 22851 AN XY: 74380

Gnomad4 AFR AF: 0.581

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.579

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.318

Alfa AF: 0.192 Hom.: 3701

Bravo AF: 0.330

Asia WGS AF: 0.413 AC: 1437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.36

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

Other links and lift over

dbSNP: rs2985; hg19: chr6-34845648;