Variant 15-74589834-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4BP6_Very_StrongBS2

The NM_006465.4(ARID3B):c.712C>A(p.Arg238Arg) variant causes a synonymous change. The variant allele was found at a frequency of 0.00609 in 1,610,322 control chromosomes in the GnomAD database, including 34 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0042 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0063 ( 34 hom. )

Consequence

ARID3B
NM_006465.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 3.80

Variant links:

Genes affected

ARID3B (HGNC:14350): (AT-rich interaction domain 3B) This gene encodes a member of the ARID (AT-rich interaction domain) family of DNA-binding proteins. The encoded protein is homologous with two proteins that bind to the retinoblastoma gene product, and also with the mouse Bright and Drosophila dead ringer proteins. A pseudogene on chromosome 1p31 exists for this gene. Members of the ARID family have roles in embryonic patterning, cell lineage gene regulation, cell cycle control, transcriptional regulation and possibly in chromatin structure modification. [provided by RefSeq, Jul 2008]

ARID3B links:

ARID3B (HGNC:):

ARID3B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.09).

BP6

Variant 15-74589834-C-A is Benign according to our data. Variant chr15-74589834-C-A is described in ClinVar as [Benign]. Clinvar id is 777463.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High AC in GnomAd4 at 644 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARID3B	NM_006465.4 linkuse as main transcript	c.712C>A	p.Arg238Arg	synonymous_variant	5/9	ENST00000346246.10	NP_006456.1	Q8IVW6-4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
ARID3B	ENST00000346246.10 linkuse as main transcript	c.712C>A	p.Arg238Arg	synonymous_variant	5/9	1	NM_006465.4	ENSP00000343126.5	Q8IVW6-4
ARID3B	ENST00000622429.1 linkuse as main transcript	c.712C>A	p.Arg238Arg	synonymous_variant	5/9	1		ENSP00000477878.1	Q8IVW6-1
ARID3B	ENST00000566147.1 linkuse as main transcript	c.-12C>A		5_prime_UTR_variant	2/3	3		ENSP00000455668.1	H3BQ92

Frequencies

GnomAD3 genomes

AF:

0.00423

AC:

644

AN:

152194

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00111

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00353

Gnomad ASJ

AF:

0.00461

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00415

Gnomad FIN

AF:

0.00452

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00667

Gnomad OTH

AF:

0.00287

GnomAD3 exomes

AF:

0.00423

AC:

1056

AN:

249896

Hom.:

AF XY:

0.00390

AC XY:

527

AN XY:

135080

show subpopulations

Gnomad AFR exome

AF:

0.000924

Gnomad AMR exome

AF:

0.00234

Gnomad ASJ exome

AF:

0.00291

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.00180

Gnomad FIN exome

AF:

0.00532

Gnomad NFE exome

AF:

0.00648

Gnomad OTH exome

AF:

0.00460

GnomAD4 exome

AF:

0.00629

AC:

9170

AN:

1458010

Hom.:

Cov.:

AF XY:

0.00605

AC XY:

4388

AN XY:

725116

show subpopulations

Gnomad4 AFR exome

AF:

0.000930

Gnomad4 AMR exome

AF:

0.00284

Gnomad4 ASJ exome

AF:

0.00227

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.00252

Gnomad4 FIN exome

AF:

0.00587

Gnomad4 NFE exome

AF:

0.00727

Gnomad4 OTH exome

AF:

0.00567

GnomAD4 genome

AF:

0.00423

AC:

644

AN:

152312

Hom.:

Cov.:

AF XY:

0.00422

AC XY:

314

AN XY:

74486

show subpopulations

Gnomad4 AFR

AF:

0.00111

Gnomad4 AMR

AF:

0.00353

Gnomad4 ASJ

AF:

0.00461

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00416

Gnomad4 FIN

AF:

0.00452

Gnomad4 NFE

AF:

0.00667

Gnomad4 OTH

AF:

0.00284

Alfa

AF:

0.00429

Hom.:

Bravo

AF:

0.00396

Asia WGS

AF:

0.000289

AC:

AN:

3478

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	Labcorp Genetics (formerly Invitae), Labcorp	Nov 15, 2017	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.090

CADD

Benign

DANN

Benign

0.73

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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