rs9381135

chr6-42083085-C-T

Variant summary

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

The NM_138572.3(TAF8):c.*5540C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,190 control chromosomes in the GnomAD database, including 1,380 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 0.13 (1380 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: TAF8 NM_138572.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.501

Genes affected

TAF8 (HGNC:17300): (TATA-box binding protein associated factor 8) This gene encodes one of several TATA-binding protein (TBP)-associated factors (TAFs), which are integral subunits of the general transcription factor complex TFIID. TFIID recognizes the core promoter of many genes and nucleates the assembly of a transcription preinitiation complex containing RNA polymerase II and other initiation factors. The protein encoded by this gene contains an H4-like histone fold domain, and interacts with several subunits of TFIID including TBP and the histone-fold protein TAF10. Alternatively spliced transcript variants have been described, but their biological validity has not been determined. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TAF8	NM_138572.3	c.*5540C>T		3_prime_UTR_variant	9/9	ENST00000372977.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TAF8	ENST00000372977.8	c.*5540C>T		3_prime_UTR_variant	9/9	1	NM_138572.3	P4

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19898 AN: 152072 Hom.: 1382 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.0859

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.0876

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.131 AC: 19914 AN: 152190 Hom.: 1380 Cov.: 32 AF XY: 0.130 AC XY: 9666 AN XY: 74408

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.0855

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.241

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.0876

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.130

Alfa AF: 0.125 Hom.: 982

Bravo AF: 0.131

Asia WGS AF: 0.218 AC: 758 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	3.3
Dann	Benign	0.59

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs9381135; hg19: chr6-42050823;