10-7845658-G-A

Position:

• chr10-7845658-G-A

Variant summary

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

The NM_031923.4(TAF3):​c.409+21098G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0826 in 146,774 control chromosomes in the GnomAD database, including 615 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 0.083 (615 hom., cov: 32)
• Consequence: TAF3 NM_031923.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.610

Genes affected

TAF3 (HGNC:17303): (TATA-box binding protein associated factor 3) The highly conserved RNA polymerase II transcription factor TFIID (see TAF1; MIM 313650) comprises the TATA box-binding protein (TBP; MIM 600075) and a set of TBP-associated factors (TAFs), including TAF3. TAFs contribute to promoter recognition and selectivity and act as antiapoptotic factors (Gangloff et al., 2001 [PubMed 11438666]).[supplied by OMIM, May 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TAF3	NM_031923.4	c.409+21098G>A		intron_variant		ENST00000344293.6
TAF3	XM_011519741.2	c.409+21098G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TAF3	ENST00000344293.6	c.409+21098G>A		intron_variant		1	NM_031923.4	P4

Frequencies

GnomAD3 genomes AF: 0.0826 AC: 12109 AN: 146656 Hom.: 613 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.0190

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.0546

Gnomad EAS AF: 0.0731

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.0187

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0621

Gnomad OTH AF: 0.0911

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

GnomAD4 genome AF: 0.0826 AC: 12119 AN: 146774 Hom.: 615 Cov.: 32 AF XY: 0.0812 AC XY: 5819 AN XY: 71634

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.0546

Gnomad4 EAS AF: 0.0734

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.0187

Gnomad4 NFE AF: 0.0621

Gnomad4 OTH AF: 0.0896

Alfa AF: 0.0751 Hom.: 404

Bravo AF: 0.0902

Asia WGS AF: 0.104 AC: 353 AN: 3400

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	9.7
DANN	Benign	0.68

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs11255400; hg19: chr10-7887621;