Genetic Variant NM_001002860.4:c.2122-14_2122-13delTT (chr14-93246298-TAA-T) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001002860.4(BTBD7):c.2122-14_2122-13delTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 1,336,614 control chromosomes in the GnomAD database, including 10,800 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.31 ( 5439 hom., cov: 0)

Exomes 𝑓: 0.25 ( 5361 hom. )

Consequence

BTBD7
NM_001002860.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.08

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: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BTBD7	NM_001002860.4 link	c.2122-14_2122-13delTT		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.2122-14_2122-13delTT	intron_variant	Intron 9 of 10	1	NM_001002860.4	ENSP00000335615.5	Q9P203-1
BTBD7	ENST00000554565.5 link	c.1069-14_1069-13delTT	intron_variant	Intron 7 of 8	1		ENSP00000451010.1	Q9P203-5
BTBD7	ENST00000553975.1 link	c.967-14_967-13delTT	intron_variant	Intron 5 of 6	2		ENSP00000450778.1	H0YJ41
BTBD7	ENST00000355125.3 link	n.743-14_743-13delTT	intron_variant	Intron 6 of 7	2		ENSP00000347246.3	H3BLV3

Frequencies

GnomAD3 genomes

AF:

0.314

AC:

44943

AN:

143282

Hom.:

5427

Cov.:

show subpopulations

Gnomad AFR

AF:

0.450

Gnomad AMI

AF:

0.272

Gnomad AMR

AF:

0.258

Gnomad ASJ

AF:

0.286

Gnomad EAS

AF:

0.302

Gnomad SAS

AF:

0.336

Gnomad FIN

AF:

0.254

Gnomad MID

AF:

0.291

Gnomad NFE

AF:

0.253

Gnomad OTH

AF:

0.313

GnomAD2 exomes

AF:

0.285

AC:

30854

AN:

108090

AF XY:

0.283

show subpopulations

Gnomad AFR exome

AF:

0.416

Gnomad AMR exome

AF:

0.265

Gnomad ASJ exome

AF:

0.302

Gnomad EAS exome

AF:

0.317

Gnomad FIN exome

AF:

0.257

Gnomad NFE exome

AF:

0.262

Gnomad OTH exome

AF:

0.284

GnomAD4 exome

AF:

0.247

AC:

294245

AN:

1193252

Hom.:

5361

AF XY:

0.247

AC XY:

143182

AN XY:

578980

show subpopulations

African (AFR)

AF:

0.395

AC:

10533

AN:

26660

American (AMR)

AF:

0.259

AC:

5544

AN:

21438

Ashkenazi Jewish (ASJ)

AF:

0.261

AC:

4463

AN:

17082

East Asian (EAS)

AF:

0.317

AC:

10968

AN:

34568

South Asian (SAS)

AF:

0.308

AC:

14207

AN:

46150

European-Finnish (FIN)

AF:

0.241

AC:

9675

AN:

40086

Middle Eastern (MID)

AF:

0.248

AC:

1156

AN:

4664

European-Non Finnish (NFE)

AF:

0.236

AC:

225044

AN:

953472

Other (OTH)

AF:

0.258

AC:

12655

AN:

49132

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.429

Heterozygous variant carriers

10657

21313

31970

42626

53283

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9346

18692

28038

37384

46730

<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:

0.314

AC:

45004

AN:

143362

Hom.:

5439

Cov.:

AF XY:

0.312

AC XY:

21731

AN XY:

69618

show subpopulations

African (AFR)

AF:

0.451

AC:

17693

AN:

39258

American (AMR)

AF:

0.258

AC:

3722

AN:

14428

Ashkenazi Jewish (ASJ)

AF:

0.286

AC:

948

AN:

3318

East Asian (EAS)

AF:

0.302

AC:

1503

AN:

4978

South Asian (SAS)

AF:

0.336

AC:

1532

AN:

4564

European-Finnish (FIN)

AF:

0.254

AC:

2266

AN:

8924

Middle Eastern (MID)

AF:

0.301

AC:

AN:

276

European-Non Finnish (NFE)

AF:

0.253

AC:

16386

AN:

64738

Other (OTH)

AF:

0.316

AC:

632

AN:

1998

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.522

Heterozygous variant carriers

1441

2881

4322

5762

7203

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

470

940

1410

1880

2350

<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:

0.136

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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