10-7824594-T-C

Variant names:

• chr10-7824594-T-C
• rs1244471
• NM_031923.4:c.409+34T>C

Variant summary

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

The NM_031923.4(TAF3):​c.409+34T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.546 in 1,599,604 control chromosomes in the GnomAD database, including 241,782 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 (23334 hom., cov: 34)
  • Exomes 𝑓: 0.55 (218448 hom.)
• Consequence: TAF3 NM_031923.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.415

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 (EAS) allele frequency at 95% confidence interval = 0.761 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAF3	NM_031923.4	c.409+34T>C		intron_variant	Intron 2 of 6	ENST00000344293.6	NP_114129.1
TAF3	XM_011519741.2	c.409+34T>C		intron_variant	Intron 2 of 6		XP_011518043.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAF3	ENST00000344293.6	c.409+34T>C		intron_variant	Intron 2 of 6	1	NM_031923.4	ENSP00000340271.5

Frequencies

GnomAD3 genomes AF: 0.551 AC: 83811 AN: 152012 Hom.: 23327 Cov.: 34

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.782

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.536

GnomAD3 exomes AF: 0.573 AC: 139997 AN: 244346 Hom.: 41177 AF XY: 0.579 AC XY: 76797 AN XY: 132644

Gnomad AFR exome AF: 0.544

Gnomad AMR exome AF: 0.531

Gnomad ASJ exome AF: 0.546

Gnomad EAS exome AF: 0.774

Gnomad SAS exome AF: 0.712

Gnomad FIN exome AF: 0.569

Gnomad NFE exome AF: 0.524

Gnomad OTH exome AF: 0.553

GnomAD4 exome AF: 0.545 AC: 789168 AN: 1447474 Hom.: 218448 Cov.: 31 AF XY: 0.550 AC XY: 395501 AN XY: 718872

Gnomad4 AFR exome AF: 0.541

Gnomad4 AMR exome AF: 0.532

Gnomad4 ASJ exome AF: 0.547

Gnomad4 EAS exome AF: 0.799

Gnomad4 SAS exome AF: 0.701

Gnomad4 FIN exome AF: 0.566

Gnomad4 NFE exome AF: 0.522

Gnomad4 OTH exome AF: 0.562

GnomAD4 genome AF: 0.551 AC: 83855 AN: 152130 Hom.: 23334 Cov.: 34 AF XY: 0.556 AC XY: 41372 AN XY: 74388

Gnomad4 AFR AF: 0.537

Gnomad4 AMR AF: 0.545

Gnomad4 ASJ AF: 0.546

Gnomad4 EAS AF: 0.781

Gnomad4 SAS AF: 0.701

Gnomad4 FIN AF: 0.569

Gnomad4 NFE AF: 0.532

Gnomad4 OTH AF: 0.540

Alfa AF: 0.529 Hom.: 22062

Bravo AF: 0.541

Asia WGS AF: 0.741 AC: 2576 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.1
DANN	Benign	0.74

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: rs1244471; hg19: chr10-7866557; COSMIC: COSV60210899;