rs10491309

Variant names:

• chr5-141299458-A-G
• rs10491309
• ENST00000624699.1:n.128+21060T>C

Variant summary

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

The ENST00000624699.1(TAF7):​n.128+21060T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0648 in 152,318 control chromosomes in the GnomAD database, including 345 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 0.065 (345 hom., cov: 33)
• Consequence: TAF7 ENST00000624699.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.715

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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0667 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAF7	ENST00000624699.1	n.128+21060T>C		intron_variant	Intron 1 of 2	3
TAF7	ENST00000686518.1	n.75+21060T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0649 AC: 9875 AN: 152200 Hom.: 345 Cov.: 33

Gnomad AFR AF: 0.0663

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0661

Gnomad ASJ AF: 0.0548

Gnomad EAS AF: 0.0177

Gnomad SAS AF: 0.0354

Gnomad FIN AF: 0.0741

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0684

Gnomad OTH AF: 0.0770

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

GnomAD4 genome AF: 0.0648 AC: 9877 AN: 152318 Hom.: 345 Cov.: 33 AF XY: 0.0645 AC XY: 4806 AN XY: 74488

Gnomad4 AFR AF: 0.0663

Gnomad4 AMR AF: 0.0659

Gnomad4 ASJ AF: 0.0548

Gnomad4 EAS AF: 0.0177

Gnomad4 SAS AF: 0.0354

Gnomad4 FIN AF: 0.0741

Gnomad4 NFE AF: 0.0684

Gnomad4 OTH AF: 0.0771

Alfa AF: 0.0677 Hom.: 340

Bravo AF: 0.0655

Asia WGS AF: 0.0200 AC: 72 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	16
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10491309; hg19: chr5-140679023;