Variant 1-92147696-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_001376131.1(BTBD8):c.1032G>A(p.Lys344Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00292 in 1,607,862 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0020 ( 1 hom., cov: 32)

Exomes 𝑓: 0.0030 ( 13 hom. )

Consequence

BTBD8
NM_001376131.1 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.36

Variant links:

Genes affected

BTBD8 (HGNC:21019): (BTB domain containing 8) Predicted to be involved in clathrin-dependent synaptic vesicle endocytosis; neuron projection development; and synaptic vesicle budding from endosome. Located in nucleoplasm. Colocalizes with AP-2 adaptor complex. [provided by Alliance of Genome Resources, Apr 2022]

BTBD8 links:

BTBD8 (HGNC:):

BTBD8 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.42).

BP6

Variant 1-92147696-G-A is Benign according to our data. Variant chr1-92147696-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2638929.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=2.36 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 13 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BTBD8	NM_001376131.1 linkuse as main transcript	c.1032G>A	p.Lys344Lys	synonymous_variant	9/18	ENST00000636805.2	NP_001363060.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BTBD8	ENST00000636805.2 linkuse as main transcript	c.1032G>A	p.Lys344Lys	synonymous_variant	9/18	5	NM_001376131.1	ENSP00000490161.1		Q5XKL5-3

Frequencies

GnomAD3 genomes

AF:

0.00204

AC:

310

AN:

152090

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000580

Gnomad AMI

AF:

0.00768

Gnomad AMR

AF:

0.00151

Gnomad ASJ

AF:

0.000866

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000831

Gnomad FIN

AF:

0.000661

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00353

Gnomad OTH

AF:

0.000956

GnomAD3 exomes

AF:

0.00217

AC:

533

AN:

245364

Hom.:

AF XY:

0.00223

AC XY:

295

AN XY:

132310

show subpopulations

Gnomad AFR exome

AF:

0.000681

Gnomad AMR exome

AF:

0.000993

Gnomad ASJ exome

AF:

0.000610

Gnomad EAS exome

AF:

0.0000551

Gnomad SAS exome

AF:

0.00169

Gnomad FIN exome

AF:

0.000511

Gnomad NFE exome

AF:

0.00363

Gnomad OTH exome

AF:

0.00268

GnomAD4 exome

AF:

0.00301

AC:

4381

AN:

1455654

Hom.:

Cov.:

AF XY:

0.00301

AC XY:

2175

AN XY:

723774

show subpopulations

Gnomad4 AFR exome

AF:

0.000632

Gnomad4 AMR exome

AF:

0.00108

Gnomad4 ASJ exome

AF:

0.000617

Gnomad4 EAS exome

AF:

0.0000253

Gnomad4 SAS exome

AF:

0.00150

Gnomad4 FIN exome

AF:

0.000920

Gnomad4 NFE exome

AF:

0.00360

Gnomad4 OTH exome

AF:

0.00199

GnomAD4 genome

AF:

0.00204

AC:

310

AN:

152208

Hom.:

Cov.:

AF XY:

0.00181

AC XY:

135

AN XY:

74426

show subpopulations

Gnomad4 AFR

AF:

0.000578

Gnomad4 AMR

AF:

0.00150

Gnomad4 ASJ

AF:

0.000866

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000831

Gnomad4 FIN

AF:

0.000661

Gnomad4 NFE

AF:

0.00353

Gnomad4 OTH

AF:

0.000946

Alfa

AF:

0.00262

Hom.:

Bravo

AF:

0.00199

Asia WGS

AF:

0.000578

AC:

AN:

3476

EpiCase

AF:

0.00267

EpiControl

AF:

0.00296

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jan 01, 2023

BTBD8: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.42

CADD

Benign

6.5

DANN

Benign

0.60

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