Genetic Variant NM_001002860.4:c.2122-16_2122-13delTTTT (chr14-93246298-TAAAA-T) – 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.2122-16_2122-13delTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00024 in 1,207,038 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00024 ( 0 hom. )

Failed GnomAD Quality Control

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: 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.2122-16_2122-13delTTTT		intron	N/A	NP_001002860.2	Q9P203-1
	BTBD7	NM_001289133.2		c.1069-16_1069-13delTTTT		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.2122-16_2122-13delTTTT	intron	N/A	ENSP00000335615.5	Q9P203-1
BTBD7	ENST00000554565.5	TSL:1	c.1069-16_1069-13delTTTT	intron	N/A	ENSP00000451010.1	Q9P203-5
BTBD7	ENST00000893710.1		c.2122-16_2122-13delTTTT	intron	N/A	ENSP00000563769.1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

142556

Hom.:

Cov.:

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.000657

AC:

AN:

108090

AF XY:

0.000751

show subpopulations

Gnomad AFR exome

AF:

0.000796

Gnomad AMR exome

AF:

0.000527

Gnomad ASJ exome

AF:

0.000970

Gnomad EAS exome

AF:

0.000413

Gnomad FIN exome

AF:

0.0000918

Gnomad NFE exome

AF:

0.000681

Gnomad OTH exome

AF:

0.000894

GnomAD4 exome

AF:

0.000240

AC:

290

AN:

1207038

Hom.:

AF XY:

0.000273

AC XY:

160

AN XY:

585610

show subpopulations

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

African (AFR)

AF:

0.000149

AC:

AN:

26812

American (AMR)

AF:

0.000231

AC:

AN:

21658

Ashkenazi Jewish (ASJ)

AF:

0.000348

AC:

AN:

17252

East Asian (EAS)

AF:

0.000229

AC:

AN:

34878

South Asian (SAS)

AF:

0.00139

AC:

AN:

46630

European-Finnish (FIN)

AF:

0.000222

AC:

AN:

40480

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4702

European-Non Finnish (NFE)

AF:

0.000185

AC:

179

AN:

965028

Other (OTH)

AF:

0.000282

AC:

AN:

49598

⚠️ 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: 0.278

Heterozygous variant carriers

107

134

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome 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

GnomAD4 genome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

142556

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

69148

African (AFR)

AF:

0.00

AC:

AN:

39054

American (AMR)

AF:

0.00

AC:

AN:

14280

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3296

East Asian (EAS)

AF:

0.00

AC:

AN:

4940

South Asian (SAS)

AF:

0.00

AC:

AN:

4532

European-Finnish (FIN)

AF:

0.00

AC:

AN:

8858

Middle Eastern (MID)

AF:

0.00

AC:

AN:

300

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

64448

Other (OTH)

AF:

0.00

AC:

AN:

1972

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over