Genetic Variant NM_001002860.4: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:

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ACMG classification

Classification was made for transcript

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BTBD7	NM_001002860.4 link	c.2122-13dupT		intron_variant	Intron 9 of 10	ENST00000334746.10	NP_001002860.2	Q9P203-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
BTBD7	ENST00000334746.10 link	c.2122-13_2122-12insT	intron_variant	Intron 9 of 10	1	NM_001002860.4	ENSP00000335615.5	Q9P203-1
BTBD7	ENST00000554565.5 link	c.1069-13_1069-12insT	intron_variant	Intron 7 of 8	1		ENSP00000451010.1	Q9P203-5
BTBD7	ENST00000553975.1 link	c.967-13_967-12insT	intron_variant	Intron 5 of 6	2		ENSP00000450778.1	H0YJ41
BTBD7	ENST00000355125.3 link	n.743-13_743-12insT	intron_variant	Intron 6 of 7	2		ENSP00000347246.3	H3BLV3

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 v4.3

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

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