Variant 15-74589911-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2

The NM_006465.4(ARID3B):c.789G>A(p.Val263=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00209 in 1,614,104 control chromosomes in the GnomAD database, including 26 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0028 ( 5 hom., cov: 32)

Exomes 𝑓: 0.0020 ( 21 hom. )

Consequence

ARID3B
NM_006465.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.52

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:

LOC124903527 (HGNC:):

LOC124903527 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.38).

BP6

Variant 15-74589911-G-A is Benign according to our data. Variant chr15-74589911-G-A is described in ClinVar as [Benign]. Clinvar id is 782339.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=2.52 with no splicing effect.

BS1

Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00282 (429/152242) while in subpopulation EAS AF= 0.0241 (125/5182). AF 95% confidence interval is 0.0207. There are 5 homozygotes in gnomad4. There are 223 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High AC in GnomAd4 at 429 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARID3B	NM_006465.4 linkuse as main transcript	c.789G>A	p.Val263=	synonymous_variant	5/9	ENST00000346246.10
LOC124903527	XR_007064718.1 linkuse as main transcript	n.802C>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARID3B	ENST00000346246.10 linkuse as main transcript	c.789G>A	p.Val263=	synonymous_variant	5/9	1	NM_006465.4	P4	Q8IVW6-4
ARID3B	ENST00000622429.1 linkuse as main transcript	c.789G>A	p.Val263=	synonymous_variant	5/9	1		A2	Q8IVW6-1
ARID3B	ENST00000566147.1 linkuse as main transcript	c.66G>A	p.Val22=	synonymous_variant	2/3	3

Frequencies

GnomAD3 genomes

AF:

0.00284

AC:

432

AN:

152124

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000435

Gnomad AMI

AF:

0.118

Gnomad AMR

AF:

0.00118

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0246

Gnomad SAS

AF:

0.000831

Gnomad FIN

AF:

0.00603

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00132

Gnomad OTH

AF:

0.000955

GnomAD3 exomes

AF:

0.00333

AC:

838

AN:

251474

Hom.:

AF XY:

0.00316

AC XY:

429

AN XY:

135918

show subpopulations

Gnomad AFR exome

AF:

0.000492

Gnomad AMR exome

AF:

0.000376

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0268

Gnomad SAS exome

AF:

0.000882

Gnomad FIN exome

AF:

0.00670

Gnomad NFE exome

AF:

0.00120

Gnomad OTH exome

AF:

0.00244

GnomAD4 exome

AF:

0.00202

AC:

2952

AN:

1461862

Hom.:

Cov.:

AF XY:

0.00196

AC XY:

1422

AN XY:

727238

show subpopulations

Gnomad4 AFR exome

AF:

0.000239

Gnomad4 AMR exome

AF:

0.000358

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0217

Gnomad4 SAS exome

AF:

0.000719

Gnomad4 FIN exome

AF:

0.00691

Gnomad4 NFE exome

AF:

0.00130

Gnomad4 OTH exome

AF:

0.00301

GnomAD4 genome

AF:

0.00282

AC:

429

AN:

152242

Hom.:

Cov.:

AF XY:

0.00300

AC XY:

223

AN XY:

74418

show subpopulations

Gnomad4 AFR

AF:

0.000433

Gnomad4 AMR

AF:

0.00118

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.0241

Gnomad4 SAS

AF:

0.000831

Gnomad4 FIN

AF:

0.00603

Gnomad4 NFE

AF:

0.00132

Gnomad4 OTH

AF:

0.000945

Alfa

AF:

0.00123

Hom.:

Bravo

AF:

0.00293

Asia WGS

AF:

0.0110

AC:

AN:

3478

EpiCase

AF:

0.00104

EpiControl

AF:

0.000830

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

Invitae

Jan 05, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.38

CADD

Benign

8.5

DANN

Benign

0.71

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