6-34877672-T-G

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.454

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=-0.9).
• 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/exons	MANE	UniProt
TAF11	NM_005643.4	c.*918A>C		3_prime_UTR_variant	5/5	ENST00000361288.9
TAF11	XM_011514827.3	c.*918A>C		3_prime_UTR_variant	5/5
TAF11	XM_047419270.1	c.*992A>C		3_prime_UTR_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TAF11	ENST00000361288.9	c.*918A>C		3_prime_UTR_variant	5/5	1	NM_005643.4	P1
TAF11	ENST00000650109.1	c.*1062A>C		3_prime_UTR_variant	6/6
TAF11	ENST00000693593.1	c.*1842A>C		3_prime_UTR_variant, NMD_transcript_variant	5/5

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69367 AN: 151678 Hom.: 20721 Cov.: 31

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: 75 AN: 348 Hom.: 13 Cov.: 0 AF XY: 0.226 AC XY: 48 AN XY: 212

Gnomad4 FIN exome AF: 0.213

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.458 AC: 69471 AN: 151796 Hom.: 20778 Cov.: 31 AF XY: 0.457 AC XY: 33868 AN XY: 74162

Gnomad4 AFR AF: 0.831

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.482

Gnomad4 EAS AF: 0.696

Gnomad4 SAS AF: 0.423

Gnomad4 FIN AF: 0.211

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.491

Alfa AF: 0.312 Hom.: 10309

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
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4646949; hg19: chr6-34845449;