Genetic Variant TAF3:c.409+34T>C (chr10-7824594-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.415

Publications

9 publications found

Variant links:

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]

TAF3 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031923.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAF3	NM_031923.4	MANE Select	c.409+34T>C		intron	N/A	NP_114129.1	Q5VWG9

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TAF3	ENST00000344293.6	TSL:1 MANE Select	c.409+34T>C	intron	N/A	ENSP00000340271.5	Q5VWG9
TAF3	ENST00000687522.1		c.409+34T>C	intron	N/A	ENSP00000508875.1	A0A8I5KR98
TAF3	ENST00000685647.1		n.648T>C	non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.551

AC:

83811

AN:

152012

Hom.:

23327

Cov.:

show subpopulations

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

GnomAD2 exomes

AF:

0.573

AC:

139997

AN:

244346

AF XY:

0.579

show subpopulations

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 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.:

AF XY:

0.550

AC XY:

395501

AN XY:

718872

show subpopulations

African (AFR)

AF:

0.541

AC:

17860

AN:

32996

American (AMR)

AF:

0.532

AC:

23237

AN:

43698

Ashkenazi Jewish (ASJ)

AF:

0.547

AC:

14012

AN:

25632

East Asian (EAS)

AF:

0.799

AC:

31578

AN:

39524

South Asian (SAS)

AF:

0.701

AC:

59749

AN:

85206

European-Finnish (FIN)

AF:

0.566

AC:

29870

AN:

52782

Middle Eastern (MID)

AF:

0.599

AC:

3413

AN:

5702

European-Non Finnish (NFE)

AF:

0.522

AC:

575831

AN:

1102130

Other (OTH)

AF:

0.562

AC:

33618

AN:

59804

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.476

Heterozygous variant carriers

15667

31333

47000

62666

78333

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

16710

33420

50130

66840

83550

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.551

AC:

83855

AN:

152130

Hom.:

23334

Cov.:

AF XY:

0.556

AC XY:

41372

AN XY:

74388

show subpopulations

African (AFR)

AF:

0.537

AC:

22283

AN:

41510

American (AMR)

AF:

0.545

AC:

8338

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.546

AC:

1897

AN:

3472

East Asian (EAS)

AF:

0.781

AC:

4045

AN:

5178

South Asian (SAS)

AF:

0.701

AC:

3376

AN:

4816

European-Finnish (FIN)

AF:

0.569

AC:

6020

AN:

10578

Middle Eastern (MID)

AF:

0.571

AC:

168

AN:

294

European-Non Finnish (NFE)

AF:

0.532

AC:

36172

AN:

67976

Other (OTH)

AF:

0.540

AC:

1138

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1957

3914

5870

7827

9784

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

730

1460

2190

2920

3650

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.530

Hom.:

33846

Bravo

AF:

0.541

Asia WGS

AF:

0.741

AC:

2576

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

5.1

(source)

DANN

Benign

0.74

PhyloP100

-0.41

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over