Genetic Variant BTBD7:c.2122-13dupT (chr14-93246298-T-TA) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001002860.4(BTBD7):c.2122-13dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00079 ( 0 hom., cov: 0)

Exomes 𝑓: 0.012 ( 0 hom. )

Consequence

BTBD7
NM_001002860.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.796

Publications

0 publications found

Variant links:

Genes affected

BTBD7 (HGNC:18269): (BTB domain containing 7) Predicted to be involved in regulation of branching involved in salivary gland morphogenesis. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

BTBD7 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001002860.4. 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
	BTBD7	NM_001002860.4	MANE Select	c.2122-13dupT		intron	N/A	NP_001002860.2	Q9P203-1
	BTBD7	NM_001289133.2		c.1069-13dupT		intron	N/A	NP_001276062.1	Q9P203-5

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
BTBD7	ENST00000334746.10	TSL:1 MANE Select	c.2122-13_2122-12insT	intron	N/A	ENSP00000335615.5	Q9P203-1
BTBD7	ENST00000554565.5	TSL:1	c.1069-13_1069-12insT	intron	N/A	ENSP00000451010.1	Q9P203-5
BTBD7	ENST00000893710.1		c.2122-13_2122-12insT	intron	N/A	ENSP00000563769.1

Frequencies

GnomAD3 genomes

AF:

0.000793

AC:

113

AN:

142550

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000179

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00343

Gnomad ASJ

AF:

0.00485

Gnomad EAS

AF:

0.000405

Gnomad SAS

AF:

0.000883

Gnomad FIN

AF:

0.00113

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000372

Gnomad OTH

AF:

0.000507

GnomAD2 exomes

AF:

0.0110

AC:

1189

AN:

108090

AF XY:

0.0103

show subpopulations

Gnomad AFR exome

AF:

0.00659

Gnomad AMR exome

AF:

0.0117

Gnomad ASJ exome

AF:

0.0136

Gnomad EAS exome

AF:

0.0120

Gnomad FIN exome

AF:

0.00743

Gnomad NFE exome

AF:

0.0121

Gnomad OTH exome

AF:

0.0139

GnomAD4 exome

AF:

0.0123

AC:

14710

AN:

1192188

Hom.:

Cov.:

AF XY:

0.0122

AC XY:

7043

AN XY:

578668

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.00576

AC:

154

AN:

26728

American (AMR)

AF:

0.00853

AC:

184

AN:

21560

Ashkenazi Jewish (ASJ)

AF:

0.0126

AC:

215

AN:

17124

East Asian (EAS)

AF:

0.00558

AC:

194

AN:

34794

South Asian (SAS)

AF:

0.0145

AC:

674

AN:

46476

European-Finnish (FIN)

AF:

0.00793

AC:

319

AN:

40216

Middle Eastern (MID)

AF:

0.00599

AC:

AN:

4672

European-Non Finnish (NFE)

AF:

0.0130

AC:

12389

AN:

951514

Other (OTH)

AF:

0.0113

AC:

553

AN:

49104

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.264

Heterozygous variant carriers

1644

3288

4931

6575

8219

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

524

1048

1572

2096

2620

<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:

0.000792

AC:

113

AN:

142632

Hom.:

Cov.:

AF XY:

0.000924

AC XY:

AN XY:

69242

show subpopulations

African (AFR)

AF:

0.000204

AC:

AN:

39152

American (AMR)

AF:

0.00343

AC:

AN:

14302

Ashkenazi Jewish (ASJ)

AF:

0.00485

AC:

AN:

3296

East Asian (EAS)

AF:

0.000406

AC:

AN:

4926

South Asian (SAS)

AF:

0.000663

AC:

AN:

4524

European-Finnish (FIN)

AF:

0.00113

AC:

AN:

8858

Middle Eastern (MID)

AF:

0.00

AC:

AN:

274

European-Non Finnish (NFE)

AF:

0.000372

AC:

AN:

64432

Other (OTH)

AF:

0.000502

AC:

AN:

1992

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.470

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<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:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.80

Mutation Taster

=100/0

polymorphism

(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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

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