Variant 20-11923006-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_014962.4(BTBD3):c.909G>A(p.Ala303Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.057 in 1,614,150 control chromosomes in the GnomAD database, including 4,043 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.054 ( 369 hom., cov: 33)

Exomes 𝑓: 0.057 ( 3674 hom. )

Consequence

BTBD3
NM_014962.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.908

Variant links:

Genes affected

BTBD3 (HGNC:15854): (BTB domain containing 3) Enables identical protein binding activity. Predicted to be involved in cerebral cortex development and dendrite morphogenesis. Predicted to be located in nucleus. Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

BTBD3 links:

BTBD3 (HGNC:):

BTBD3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 20-11923006-G-A is Benign according to our data. Variant chr20-11923006-G-A is described in ClinVar as [Benign]. Clinvar id is 1226908.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.908 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BTBD3	NM_014962.4 linkuse as main transcript	c.909G>A	p.Ala303Ala	synonymous_variant	4/4	ENST00000378226.7	NP_055777.1	Q9Y2F9-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BTBD3	ENST00000378226.7 linkuse as main transcript	c.909G>A	p.Ala303Ala	synonymous_variant	4/4	1	NM_014962.4	ENSP00000367471.2		Q9Y2F9-1

Frequencies

GnomAD3 genomes

AF:

0.0538

AC:

8193

AN:

152192

Hom.:

373

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0386

Gnomad AMI

AF:

0.0143

Gnomad AMR

AF:

0.0636

Gnomad ASJ

AF:

0.0426

Gnomad EAS

AF:

0.257

Gnomad SAS

AF:

0.120

Gnomad FIN

AF:

0.0181

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0474

Gnomad OTH

AF:

0.0540

GnomAD3 exomes

AF:

0.0734

AC:

18322

AN:

249728

Hom.:

1131

AF XY:

0.0740

AC XY:

9983

AN XY:

134916

show subpopulations

Gnomad AFR exome

AF:

0.0413

Gnomad AMR exome

AF:

0.0845

Gnomad ASJ exome

AF:

0.0528

Gnomad EAS exome

AF:

0.253

Gnomad SAS exome

AF:

0.111

Gnomad FIN exome

AF:

0.0214

Gnomad NFE exome

AF:

0.0472

Gnomad OTH exome

AF:

0.0648

GnomAD4 exome

AF:

0.0573

AC:

83738

AN:

1461840

Hom.:

3674

Cov.:

AF XY:

0.0593

AC XY:

43094

AN XY:

727216

show subpopulations

Gnomad4 AFR exome

AF:

0.0377

Gnomad4 AMR exome

AF:

0.0818

Gnomad4 ASJ exome

AF:

0.0505

Gnomad4 EAS exome

AF:

0.253

Gnomad4 SAS exome

AF:

0.111

Gnomad4 FIN exome

AF:

0.0217

Gnomad4 NFE exome

AF:

0.0472

Gnomad4 OTH exome

AF:

0.0640

GnomAD4 genome

AF:

0.0538

AC:

8193

AN:

152310

Hom.:

369

Cov.:

AF XY:

0.0548

AC XY:

4081

AN XY:

74488

show subpopulations

Gnomad4 AFR

AF:

0.0385

Gnomad4 AMR

AF:

0.0637

Gnomad4 ASJ

AF:

0.0426

Gnomad4 EAS

AF:

0.258

Gnomad4 SAS

AF:

0.120

Gnomad4 FIN

AF:

0.0181

Gnomad4 NFE

AF:

0.0474

Gnomad4 OTH

AF:

0.0520

Alfa

AF:

0.0417

Hom.:

Bravo

AF:

0.0580

Asia WGS

AF:

0.165

AC:

575

AN:

3478

EpiCase

AF:

0.0526

EpiControl

AF:

0.0511

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Feb 19, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

7.5

DANN

Benign

0.86

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over