dbSNP rs11670188: BTBD2:c.407+1259T>C (chr19-2014038-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_017797.4(BTBD2):c.407+1259T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 149,768 control chromosomes in the GnomAD database, including 2,241 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.16 ( 2232 hom., cov: 27)

Exomes 𝑓: 0.23 ( 9 hom. )

Consequence

BTBD2
NM_017797.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.105

Publications

3 publications found

Variant links:

Genes affected

BTBD2 (HGNC:15504): (BTB domain containing 2) The C-terminus of the protein encoded by this gene binds topoisomerase I. The N-terminus contains a proline-rich region and a BTB/POZ domain (broad-complex, Tramtrack and bric a brac/Pox virus and Zinc finger), both of which are typically involved in protein-protein interactions. Subcellularly, the protein localizes to cytoplasmic bodies. [provided by RefSeq, Jul 2008]

BTBD2 links:

ENSG00000275468 (HGNC:):

ENSG00000275468 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BTBD2	NM_017797.4 link	c.407+1259T>C		intron_variant	Intron 1 of 8	ENST00000255608.9	NP_060267.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BTBD2	ENST00000255608.9 link	c.407+1259T>C		intron_variant	Intron 1 of 8	1	NM_017797.4	ENSP00000255608.3

Frequencies

GnomAD3 genomes

AF:

0.159

AC:

23776

AN:

149296

Hom.:

2232

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0655

Gnomad AMI

AF:

0.147

Gnomad AMR

AF:

0.179

Gnomad ASJ

AF:

0.281

Gnomad EAS

AF:

0.159

Gnomad SAS

AF:

0.0981

Gnomad FIN

AF:

0.170

Gnomad MID

AF:

0.199

Gnomad NFE

AF:

0.206

Gnomad OTH

AF:

0.193

GnomAD4 exome

AF:

0.232

AC:

AN:

354

Hom.:

Cov.:

AF XY:

0.235

AC XY:

AN XY:

272

show subpopulations

African (AFR)

AF:

0.250

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AF:

0.0385

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.233

AC:

AN:

292

Other (OTH)

AF:

0.333

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

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

AF:

0.159

AC:

23775

AN:

149414

Hom.:

2232

Cov.:

AF XY:

0.158

AC XY:

11481

AN XY:

72832

show subpopulations

African (AFR)

AF:

0.0654

AC:

2634

AN:

40290

American (AMR)

AF:

0.178

AC:

2683

AN:

15046

Ashkenazi Jewish (ASJ)

AF:

0.281

AC:

971

AN:

3458

East Asian (EAS)

AF:

0.159

AC:

791

AN:

4982

South Asian (SAS)

AF:

0.0984

AC:

463

AN:

4704

European-Finnish (FIN)

AF:

0.170

AC:

1760

AN:

10376

Middle Eastern (MID)

AF:

0.194

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.206

AC:

13880

AN:

67300

Other (OTH)

AF:

0.196

AC:

403

AN:

2058

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

930

1861

2791

3722

4652

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

254

508

762

1016

1270

<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:

0.196

Hom.:

5496

Bravo

AF:

0.159

Asia WGS

AF:

0.124

AC:

433

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

1.4

(source)

DANN

Benign

0.37

PhyloP100

-0.10

Mutation Taster

=100/0

polymorphism (auto)

(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