Genetic Variant NM_003972.3:c.254-127dupA (chr10-91942285-T-TA) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_003972.3(BTAF1):c.254-127dupA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 589,186 control chromosomes in the GnomAD database, including 17,079 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.33 ( 8066 hom., cov: 20)

Exomes 𝑓: 0.26 ( 9013 hom. )

Consequence

BTAF1
NM_003972.3 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.729

Publications

1 publications found

Variant links:

Genes affected

BTAF1 (HGNC:17307): (B-TFIID TATA-box binding protein associated factor 1) This gene encodes a TAF (TATA box-binding protein-associated factor), which associates with TBP (TATA box-binding protein) to form the B-TFIID complex that is required for transcription initiation of genes by RNA polymerase II. This TAF has DNA-dependent ATPase activity, which drives the dissociation of TBP from DNA, freeing the TBP to associate with other TATA boxes or TATA-less promoters. [provided by RefSeq, Sep 2011]

BTAF1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP6

Variant 10-91942285-T-TA is Benign according to our data. Variant chr10-91942285-T-TA is described in ClinVar as Benign. ClinVar VariationId is 1263341.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003972.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
BTAF1	NM_003972.3	MANE Select	c.254-127dupA	intron	N/A	NP_003963.1	Q2M1V9
BTAF1	NR_165090.1		n.561-127dupA	intron	N/A
BTAF1	NR_165091.1		n.561-127dupA	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
BTAF1	ENST00000265990.12	TSL:1 MANE Select	c.254-137_254-136insA	intron	N/A	ENSP00000265990.6	O14981-1
BTAF1	ENST00000928671.1		c.254-137_254-136insA	intron	N/A	ENSP00000598730.1
BTAF1	ENST00000928669.1		c.253+2219_253+2220insA	intron	N/A	ENSP00000598728.1

Frequencies

GnomAD3 genomes

AF:

0.327

AC:

44134

AN:

134792

Hom.:

8054

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0975

Gnomad AMI

AF:

0.388

Gnomad AMR

AF:

0.436

Gnomad ASJ

AF:

0.343

Gnomad EAS

AF:

0.526

Gnomad SAS

AF:

0.573

Gnomad FIN

AF:

0.496

Gnomad MID

AF:

0.291

Gnomad NFE

AF:

0.381

Gnomad OTH

AF:

0.336

GnomAD4 exome

AF:

0.255

AC:

115915

AN:

454278

Hom.:

9013

AF XY:

0.263

AC XY:

61988

AN XY:

235324

show subpopulations

African (AFR)

AF:

0.0687

AC:

882

AN:

12846

American (AMR)

AF:

0.342

AC:

5157

AN:

15072

Ashkenazi Jewish (ASJ)

AF:

0.246

AC:

2702

AN:

10970

East Asian (EAS)

AF:

0.377

AC:

7954

AN:

21088

South Asian (SAS)

AF:

0.389

AC:

14150

AN:

36376

European-Finnish (FIN)

AF:

0.325

AC:

7138

AN:

21938

Middle Eastern (MID)

AF:

0.198

AC:

361

AN:

1824

European-Non Finnish (NFE)

AF:

0.230

AC:

71759

AN:

311476

Other (OTH)

AF:

0.256

AC:

5812

AN:

22688

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.449

Heterozygous variant carriers

3240

6481

9721

12962

16202

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1224

2448

3672

4896

6120

<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:

0.327

AC:

44166

AN:

134908

Hom.:

8066

Cov.:

AF XY:

0.341

AC XY:

22183

AN XY:

65114

show subpopulations

African (AFR)

AF:

0.0976

AC:

3516

AN:

36026

American (AMR)

AF:

0.437

AC:

5628

AN:

12870

Ashkenazi Jewish (ASJ)

AF:

0.343

AC:

1088

AN:

3176

East Asian (EAS)

AF:

0.526

AC:

2486

AN:

4724

South Asian (SAS)

AF:

0.572

AC:

2381

AN:

4162

European-Finnish (FIN)

AF:

0.496

AC:

4294

AN:

8660

Middle Eastern (MID)

AF:

0.296

AC:

AN:

274

European-Non Finnish (NFE)

AF:

0.381

AC:

23780

AN:

62426

Other (OTH)

AF:

0.335

AC:

581

AN:

1736

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.464

Heterozygous variant carriers

1183

2366

3550

4733

5916

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

452

904

1356

1808

2260

<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:

0.146

Hom.:

402

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.73

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