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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BTBD7	NM_001002860.4 link	c.2122-16_2122-13delTTTT		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.2122-16_2122-13delTTTT	intron_variant	Intron 9 of 10	1	NM_001002860.4	ENSP00000335615.5	Q9P203-1
BTBD7	ENST00000554565.5 link	c.1069-16_1069-13delTTTT	intron_variant	Intron 7 of 8	1		ENSP00000451010.1	Q9P203-5
BTBD7	ENST00000553975.1 link	c.967-16_967-13delTTTT	intron_variant	Intron 5 of 6	2		ENSP00000450778.1	H0YJ41
BTBD7	ENST00000355125.3 link	n.743-16_743-13delTTTT	intron_variant	Intron 6 of 7	2		ENSP00000347246.3	H3BLV3

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 v4.3

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over