10-8005587-T-G

Position:

• chr10-8005587-T-G

Variant summary

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

The NM_031923.4(TAF3):​c.2316-3491T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 152,174 control chromosomes in the GnomAD database, including 4,069 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 0.21 (4069 hom., cov: 32)
• Consequence: TAF3 NM_031923.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.122

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=-0.7).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TAF3	NM_031923.4	c.2316-3491T>G		intron_variant		ENST00000344293.6
TAF3	XM_011519741.2	c.2313-3491T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TAF3	ENST00000344293.6	c.2316-3491T>G		intron_variant		1	NM_031923.4	P4
TAF3	ENST00000687522.1	c.2313-3491T>G		intron_variant				A1

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31529 AN: 152056 Hom.: 4053 Cov.: 32

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.0771

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.0870

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.208 AC: 31589 AN: 152174 Hom.: 4069 Cov.: 32 AF XY: 0.207 AC XY: 15420 AN XY: 74410

Gnomad4 AFR AF: 0.358

Gnomad4 AMR AF: 0.206

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.309

Gnomad4 FIN AF: 0.0870

Gnomad4 NFE AF: 0.136

Gnomad4 OTH AF: 0.201

Alfa AF: 0.159 Hom.: 3778

Bravo AF: 0.222

Asia WGS AF: 0.210 AC: 732 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	6.5
DANN	Benign	0.70

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: rs768166; hg19: chr10-8047550;