X-78136912-TACCTA-TTT

Position:

• chrX-78136912-TACCTA-TTT

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2 PM4_Supporting

The NM_015975.5(TAF9B):​c.479_481+2delTAGGTinsAA​(p.Ile160_Ala161delinsThr) variant causes a splice donor, disruptive inframe deletion, splice region, synonymous, intron change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 22)
• Consequence: TAF9B NM_015975.5 splice_donor, disruptive_inframe_deletion, splice_region, synonymous, intron
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 6.86

Genes affected

TAF9B (HGNC:17306): (TATA-box binding protein associated factor 9b) 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 protein that is similar to one of the small subunits of TFIID, TBP-associated factor 9, and is also a subunit of TFIID. TAF9 and TAF9b share some functions but also have distinct roles in the transcriptional regulatory process. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM4: Nonframeshift variant in NON repetitive region in NM_015975.5. Strenght limited to Supporting due to length of the change: 1aa.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TAF9B	NM_015975.5	c.479_481+2delTAGGTinsAA	p.Ile160_Ala161delinsThr	splice_donor_variant, disruptive_inframe_deletion, splice_region_variant, synonymous_variant, intron_variant	5/7	ENST00000341864.6	NP_057059.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TAF9B	ENST00000341864.6	c.479_481+2delTAGGTinsAA	p.Ile160_Ala161delinsThr	splice_donor_variant, disruptive_inframe_deletion, splice_region_variant, synonymous_variant, intron_variant	5/7	1	NM_015975.5	ENSP00000339917.5
TAF9B	ENST00000480681.1	n.568_570+2delTAGGTinsAA		splice_donor_variant, splice_region_variant, intron_variant, non_coding_transcript_exon_variant	4/6	3

Frequencies

GnomAD3 genomes Cov.: 22

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

GnomAD4 genome Cov.: 22

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

literature only

Center for Human Genetics, University of Leuven

Jan 01, 2015

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs875989809; hg19: chrX-77392410;