Genetic Variant NM_031923.4: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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAF3	NM_031923.4 link	c.409+34T>C		intron_variant	Intron 2 of 6	ENST00000344293.6	NP_114129.1	Q5VWG9
TAF3	XM_011519741.2 link	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 link	c.409+34T>C		intron_variant	Intron 2 of 6	1	NM_031923.4	ENSP00000340271.5		Q5VWG9

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 v4.3

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over