rs2985

Variant names:

• chr6-34877871-T-C
• rs2985
• NM_005643.4:c.*719A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 14 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TAF11	NM_005643.4	c.*719A>G		3_prime_UTR_variant	Exon 5 of 5	ENST00000361288.9	NP_005634.1
TAF11	NM_001270488.1	c.*793A>G		3_prime_UTR_variant	Exon 4 of 4		NP_001257417.1
TAF11	XM_011514827.3	c.*719A>G		3_prime_UTR_variant	Exon 5 of 5		XP_011513129.1
TAF11	XM_047419270.1	c.*793A>G		3_prime_UTR_variant	Exon 4 of 4		XP_047275226.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAF11	ENST00000361288.9	c.*719A>G		3_prime_UTR_variant	Exon 5 of 5	1	NM_005643.4	ENSP00000354633.4

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.581 AC: 24072 AN: 41452

American (AMR) AF: 0.269 AC: 4115 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1058 AN: 3466

East Asian (EAS) AF: 0.579 AC: 3003 AN: 5184

South Asian (SAS) AF: 0.308 AC: 1487 AN: 4826

European-Finnish (FIN) AF: 0.146 AC: 1551 AN: 10604

Middle Eastern (MID) AF: 0.295 AC: 86 AN: 292

European-Non Finnish (NFE) AF: 0.156 AC: 10628 AN: 68006

Other (OTH) AF: 0.318 AC: 672 AN: 2112

Alfa AF: 0.204 Hom.: 6502

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
PhyloP100		-0.77
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2985; hg19: chr6-34845648; COSMIC: COSV109411062; COSMIC: COSV109411062;