rs676832

Positions:

• chr5-141270635-T-A

Variant summary

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

The ENST00000624699.1(TAF7):​n.129-6701A>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 152,120 control chromosomes in the GnomAD database, including 2,055 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 0.16 (2055 hom., cov: 32)
• Consequence: TAF7 ENST00000624699.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.641

Genes affected

TAF7 (HGNC:11541): (TATA-box binding protein associated factor 7) The intronless gene for this transcription coactivator is located between the protocadherin beta and gamma gene clusters on chromosome 5. The protein encoded by this gene is a component of the TFIID protein complex, a complex which binds to the TATA box in class II promoters and recruits RNA polymerase II and other factors. This particular subunit interacts with the largest TFIID subunit, as well as multiple transcription activators. The protein is required for transcription by promoters targeted by RNA polymerase II. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TAF7	ENST00000624699.1	n.129-6701A>T		intron_variant, non_coding_transcript_variant		3
TAF7	ENST00000686518.1	n.76-10144A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24130 AN: 152002 Hom.: 2048 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.159 AC: 24153 AN: 152120 Hom.: 2055 Cov.: 32 AF XY: 0.158 AC XY: 11788 AN XY: 74378

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.197

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.160

Alfa AF: 0.153 Hom.: 237

Bravo AF: 0.163

Asia WGS AF: 0.180 AC: 626 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	4.0
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs676832; hg19: chr5-140650204;