Genetic Variant TAF1B:c.118-60A>G (chr2-9849313-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000263663.10(TAF1B):c.118-60A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 1,297,138 control chromosomes in the GnomAD database, including 56,937 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 0.24 ( 5002 hom., cov: 32)

Exomes 𝑓: 0.30 ( 51935 hom. )

Consequence

TAF1B
ENST00000263663.10 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.188

Publications

6 publications found

Variant links:

Genes affected

TAF1B (HGNC:11533): (TATA-box binding protein associated factor, RNA polymerase I subunit B) Initiation of transcription by RNA polymerase I requires the formation of a complex composed of the TATA-binding protein (TBP) and three TBP-associated factors (TAFs) specific for RNA polymerase I. This complex, known as SL1, binds to the core promoter of ribosomal RNA genes to position the polymerase properly and acts as a channel for regulatory signals. This gene encodes one of the SL1-specific TAFs. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2016]

TAF1B 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=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000263663.10. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
TAF1B	NM_005680.3	MANE Select	c.118-60A>G	intron	N/A	NP_005671.3
TAF1B	NM_001318976.1		c.-494-60A>G	intron	N/A	NP_001305905.1
TAF1B	NM_001318977.1		c.-494-60A>G	intron	N/A	NP_001305906.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
TAF1B	ENST00000263663.10	TSL:1 MANE Select	c.118-60A>G	intron	N/A	ENSP00000263663.4
TAF1B	ENST00000402170.5	TSL:5	n.178-60A>G	intron	N/A
TAF1B	ENST00000404869.7	TSL:5	n.163-60A>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.242

AC:

36759

AN:

151940

Hom.:

5005

Cov.:

show subpopulations

Gnomad AFR

AF:

0.118

Gnomad AMI

AF:

0.247

Gnomad AMR

AF:

0.221

Gnomad ASJ

AF:

0.255

Gnomad EAS

AF:

0.305

Gnomad SAS

AF:

0.258

Gnomad FIN

AF:

0.334

Gnomad MID

AF:

0.210

Gnomad NFE

AF:

0.301

Gnomad OTH

AF:

0.250

GnomAD4 exome

AF:

0.297

AC:

339767

AN:

1145080

Hom.:

51935

AF XY:

0.295

AC XY:

169226

AN XY:

573798

show subpopulations

African (AFR)

AF:

0.112

AC:

2654

AN:

23766

American (AMR)

AF:

0.224

AC:

4187

AN:

18662

Ashkenazi Jewish (ASJ)

AF:

0.253

AC:

5579

AN:

22092

East Asian (EAS)

AF:

0.334

AC:

11109

AN:

33304

South Asian (SAS)

AF:

0.251

AC:

15758

AN:

62854

European-Finnish (FIN)

AF:

0.331

AC:

15617

AN:

47228

Middle Eastern (MID)

AF:

0.203

AC:

1039

AN:

5124

European-Non Finnish (NFE)

AF:

0.306

AC:

270392

AN:

883116

Other (OTH)

AF:

0.274

AC:

13432

AN:

48934

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

11056

22112

33168

44224

55280

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

8492

16984

25476

33968

42460

<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:

0.242

AC:

36748

AN:

152058

Hom.:

5002

Cov.:

AF XY:

0.244

AC XY:

18097

AN XY:

74302

show subpopulations

African (AFR)

AF:

0.118

AC:

4893

AN:

41510

American (AMR)

AF:

0.221

AC:

3379

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.255

AC:

884

AN:

3470

East Asian (EAS)

AF:

0.305

AC:

1576

AN:

5170

South Asian (SAS)

AF:

0.257

AC:

1240

AN:

4818

European-Finnish (FIN)

AF:

0.334

AC:

3517

AN:

10534

Middle Eastern (MID)

AF:

0.195

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.301

AC:

20458

AN:

67962

Other (OTH)

AF:

0.246

AC:

519

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1370

2741

4111

5482

6852

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

396

792

1188

1584

1980

<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:

0.280

Hom.:

19977

Bravo

AF:

0.229

Asia WGS

AF:

0.254

AC:

886

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

5.5

(source)

DANN

Benign

0.49

PhyloP100

0.19

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over