X-71518692-CTTTTTTTTTTT-CTTTTTTTTTT

Variant names:

• chrX-71518692-CT-C
• rs41486346
• ENST00000437147.8:n.1359-9849delT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1 BS2

The ENST00000437147.8(TAF1):​n.1359-9849delT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.0033 (0 hom., 4 hem., cov: 19)
• Consequence: TAF1 ENST00000437147.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.00
• Publications: 0 publications found

Genes affected

TAF1 (HGNC:11535): (TATA-box binding protein associated factor 1) Initiation of transcription by RNA polymerase II requires the activities of more than 70 polypeptides. The protein that coordinates these activities is the basal transcription factor 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 the largest subunit of TFIID. This subunit binds to core promoter sequences encompassing the transcription start site. It also binds to activators and other transcriptional regulators, and these interactions affect the rate of transcription initiation. This subunit contains two independent protein kinase domains at the N- and C-terminals, but also possesses acetyltransferase activity and can act as a ubiquitin-activating/conjugating enzyme. Mutations in this gene result in Dystonia 3, torsion, X-linked, a dystonia-parkinsonism disorder. Alternative splicing of this gene results in multiple transcript variants. This gene is part of a complex transcription unit (TAF1/DYT3), wherein some transcript variants share exons with TAF1 as well as additional downstream DYT3 exons. [provided by RefSeq, Oct 2013]

TAF1 Gene-Disease associations (from GenCC):

• intellectual disability, X-linked, syndromic 33

  Inheritance: XL Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), G2P, Illumina
• X-linked dystonia-parkinsonism

  Inheritance: XL, Unknown Classification: STRONG, MODERATE, SUPPORTIVE, LIMITED Submitted by: Ambry Genetics, Genomics England PanelApp, Orphanet, Labcorp Genetics (formerly Invitae)
• X-linked intellectual disability-global development delay-facial dysmorphism-sacral caudal remnant syndrome

  Inheritance: XL Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.00326 (258/79160) while in subpopulation SAS AF = 0.0102 (16/1571). AF 95% confidence interval is 0.00639. There are 0 homozygotes in GnomAd4. There are 4 alleles in the male GnomAd4 subpopulation. Median coverage is 19. This position passed quality control check.
• BS2: High Hemizygotes in GnomAd4 at 4 XL,Unknown gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAF1	NR_104387.2	n.5520-9829delT		intron_variant	Intron 38 of 39
TAF1	NR_104388.2	n.5511-9829delT		intron_variant	Intron 38 of 39
TAF1	NR_104389.2	n.5418-9829delT		intron_variant	Intron 37 of 38

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAF1	ENST00000437147.8	n.1359-9849delT		intron_variant	Intron 12 of 13	1		ENSP00000406517.4
TAF1	ENST00000462588.5	n.999-9849delT		intron_variant	Intron 9 of 10	1		ENSP00000508350.1
TAF1	ENST00000467309.5	n.*107-9849delT		intron_variant	Intron 3 of 5	1		ENSP00000507353.1

Frequencies

GnomAD3 genomes AF: 0.00327 AC: 259 AN: 79193 Hom.: 0 Cov.: 19

Gnomad AFR AF: 0.00570

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00155

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00371

Gnomad SAS AF: 0.0107

Gnomad FIN AF: 0.00117

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00234

Gnomad OTH AF: 0.00389

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.00326 AC: 258 AN: 79160 Hom.: 0 Cov.: 19 AF XY: 0.000216 AC XY: 4 AN XY: 18554

African (AFR) AF: 0.00570 AC: 120 AN: 21051

American (AMR) AF: 0.00155 AC: 11 AN: 7093

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2065

East Asian (EAS) AF: 0.00372 AC: 9 AN: 2417

South Asian (SAS) AF: 0.0102 AC: 16 AN: 1571

European-Finnish (FIN) AF: 0.00117 AC: 3 AN: 2574

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 149

European-Non Finnish (NFE) AF: 0.00234 AC: 95 AN: 40677

Other (OTH) AF: 0.00386 AC: 4 AN: 1035

Alfa AF: 0.00 Hom.: 8

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs41486346; hg19: chrX-70738542;