Variant 8-20209624-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001693.4(ATP6V1B2):c.291+93T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0394 in 1,201,162 control chromosomes in the GnomAD database, including 1,242 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.043 ( 165 hom., cov: 32)

Exomes 𝑓: 0.039 ( 1077 hom. )

Consequence

ATP6V1B2
NM_001693.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.692

Variant links:

Genes affected

ATP6V1B2 (HGNC:854): (ATPase H+ transporting V1 subunit B2) This gene encodes a component of vacuolar ATPase (V-ATPase), a multisubunit enzyme that mediates acidification of eukaryotic intracellular organelles. V-ATPase dependent organelle acidification is necessary for such intracellular processes as protein sorting, zymogen activation, receptor-mediated endocytosis, and synaptic vesicle proton gradient generation. V-ATPase is composed of a cytosolic V1 domain and a transmembrane V0 domain. The V1 domain consists of three A, three B, and two G subunits, as well as a C, D, E, F, and H subunit. The V1 domain contains the ATP catalytic site. The protein encoded by this gene is one of two V1 domain B subunit isoforms and is the only B isoform highly expressed in osteoclasts. [provided by RefSeq, Jul 2008]

ATP6V1B2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP6

Variant 8-20209624-T-G is Benign according to our data. Variant chr8-20209624-T-G is described in ClinVar as [Benign]. Clinvar id is 1250071.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.064 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATP6V1B2	NM_001693.4 linkuse as main transcript	c.291+93T>G		intron_variant		ENST00000276390.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATP6V1B2	ENST00000276390.7 linkuse as main transcript	c.291+93T>G		intron_variant		1	NM_001693.4	P1

Frequencies

GnomAD3 genomes

AF:

0.0428

AC:

6503

AN:

152068

Hom.:

163

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0550

Gnomad AMI

AF:

0.0110

Gnomad AMR

AF:

0.0622

Gnomad ASJ

AF:

0.0245

Gnomad EAS

AF:

0.0702

Gnomad SAS

AF:

0.0464

Gnomad FIN

AF:

0.0283

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0323

Gnomad OTH

AF:

0.0397

GnomAD4 exome

AF:

0.0390

AC:

40872

AN:

1048976

Hom.:

1077

AF XY:

0.0387

AC XY:

20670

AN XY:

533802

show subpopulations

Gnomad4 AFR exome

AF:

0.0524

Gnomad4 AMR exome

AF:

0.0772

Gnomad4 ASJ exome

AF:

0.0275

Gnomad4 EAS exome

AF:

0.119

Gnomad4 SAS exome

AF:

0.0495

Gnomad4 FIN exome

AF:

0.0304

Gnomad4 NFE exome

AF:

0.0330

Gnomad4 OTH exome

AF:

0.0362

GnomAD4 genome

AF:

0.0428

AC:

6506

AN:

152186

Hom.:

165

Cov.:

AF XY:

0.0429

AC XY:

3191

AN XY:

74414

show subpopulations

Gnomad4 AFR

AF:

0.0549

Gnomad4 AMR

AF:

0.0625

Gnomad4 ASJ

AF:

0.0245

Gnomad4 EAS

AF:

0.0700

Gnomad4 SAS

AF:

0.0458

Gnomad4 FIN

AF:

0.0283

Gnomad4 NFE

AF:

0.0324

Gnomad4 OTH

AF:

0.0393

Alfa

AF:

0.0337

Hom.:

Bravo

AF:

0.0457

Asia WGS

AF:

0.0530

AC:

186

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 16, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

Cadd

Benign

2.0

Dann

Benign

0.72

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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