rs1284108

Positions:

• chr11-93765667-G-T

Variant summary

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

The ENST00000638767.1(ENSG00000284057):​c.675+5809G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 152,144 control chromosomes in the GnomAD database, including 24,806 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 0.55 (24806 hom., cov: 34)
• Consequence: ENSG00000284057 ENST00000638767.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629

Genes affected

ENSG00000284057 (HGNC:):

TAF1D (HGNC:28759): (TATA-box binding protein associated factor, RNA polymerase I subunit D) TAF1D is a member of the SL1 complex, which includes TBP (MIM 600075) and TAF1A (MIM 604903), TAF1B (MIM 604904), and TAF1C (MIM 604905), and plays a role in RNA polymerase I transcription (Wang et al., 2004 [PubMed 15520167]; Gorski et al., 2007 [PubMed 17318177]).[supplied by OMIM, Jun 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.68 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.93765667G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000284057	ENST00000638767.1	c.675+5809G>T		intron_variant		5		ENSP00000492220.1
TAF1D	ENST00000527690.1	c.-224+18637C>A		intron_variant		3		ENSP00000432852.1

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84311 AN: 152028 Hom.: 24791 Cov.: 34

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.690

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.641

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.554 AC: 84348 AN: 152144 Hom.: 24806 Cov.: 34 AF XY: 0.561 AC XY: 41708 AN XY: 74386

Gnomad4 AFR AF: 0.340

Gnomad4 AMR AF: 0.691

Gnomad4 ASJ AF: 0.607

Gnomad4 EAS AF: 0.642

Gnomad4 SAS AF: 0.587

Gnomad4 FIN AF: 0.673

Gnomad4 NFE AF: 0.624

Gnomad4 OTH AF: 0.572

Alfa AF: 0.615 Hom.: 59863

Bravo AF: 0.547

Asia WGS AF: 0.552 AC: 1919 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.40
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1284108; hg19: chr11-93498833;