Genetic Variant NM_005224.3:c.150G>A (chr19-929678-G-A) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_005224.3(ARID3A):c.150G>A(p.Glu50Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.597 in 1,556,210 control chromosomes in the GnomAD database, including 285,746 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.49 ( 21254 hom., cov: 33)

Exomes 𝑓: 0.61 ( 264492 hom. )

Consequence

ARID3A
NM_005224.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.174

Publications

13 publications found

Variant links:

Genes affected

ARID3A (HGNC:3031): (AT-rich interaction domain 3A) This gene encodes a member of the ARID (AT-rich interaction domain) family of DNA binding proteins. It was found by homology to the Drosophila dead ringer gene, which is important for normal embryogenesis. Other ARID family members 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]

ARID3A links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.67).

BP7

Synonymous conserved (PhyloP=0.174 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARID3A	NM_005224.3 link	c.150G>A	p.Glu50Glu	synonymous_variant	Exon 2 of 9	ENST00000263620.8	NP_005215.1	Q99856

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARID3A	ENST00000263620.8 link	c.150G>A	p.Glu50Glu	synonymous_variant	Exon 2 of 9	1	NM_005224.3	ENSP00000263620.2		Q99856
ARID3A	ENST00000585895.1 link	n.*180G>A		downstream_gene_variant		2

Frequencies

GnomAD3 genomes

AF:

0.493

AC:

74798

AN:

151864

Hom.:

21255

Cov.:

show subpopulations

Gnomad AFR

AF:

0.195

Gnomad AMI

AF:

0.573

Gnomad AMR

AF:

0.497

Gnomad ASJ

AF:

0.551

Gnomad EAS

AF:

0.642

Gnomad SAS

AF:

0.542

Gnomad FIN

AF:

0.633

Gnomad MID

AF:

0.522

Gnomad NFE

AF:

0.632

Gnomad OTH

AF:

0.506

GnomAD2 exomes

AF:

0.553

AC:

88687

AN:

160280

AF XY:

0.558

show subpopulations

Gnomad AFR exome

AF:

0.170

Gnomad AMR exome

AF:

0.468

Gnomad ASJ exome

AF:

0.554

Gnomad EAS exome

AF:

0.647

Gnomad FIN exome

AF:

0.633

Gnomad NFE exome

AF:

0.624

Gnomad OTH exome

AF:

0.576

GnomAD4 exome

AF:

0.608

AC:

854308

AN:

1404234

Hom.:

264492

Cov.:

AF XY:

0.607

AC XY:

421802

AN XY:

694922

show subpopulations

African (AFR)

AF:

0.172

AC:

5623

AN:

32698

American (AMR)

AF:

0.478

AC:

18149

AN:

37984

Ashkenazi Jewish (ASJ)

AF:

0.562

AC:

14190

AN:

25266

East Asian (EAS)

AF:

0.636

AC:

23878

AN:

37536

South Asian (SAS)

AF:

0.524

AC:

42480

AN:

80992

European-Finnish (FIN)

AF:

0.632

AC:

22156

AN:

35080

Middle Eastern (MID)

AF:

0.510

AC:

2386

AN:

4682

European-Non Finnish (NFE)

AF:

0.633

AC:

691061

AN:

1091430

Other (OTH)

AF:

0.587

AC:

34385

AN:

58566

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.474

Heterozygous variant carriers

20600

41201

61801

82402

103002

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

18316

36632

54948

73264

91580

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.492

AC:

74801

AN:

151976

Hom.:

21254

Cov.:

AF XY:

0.494

AC XY:

36720

AN XY:

74300

show subpopulations

African (AFR)

AF:

0.194

AC:

8070

AN:

41520

American (AMR)

AF:

0.497

AC:

7595

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.551

AC:

1911

AN:

3466

East Asian (EAS)

AF:

0.642

AC:

3295

AN:

5132

South Asian (SAS)

AF:

0.543

AC:

2619

AN:

4826

European-Finnish (FIN)

AF:

0.633

AC:

6703

AN:

10592

Middle Eastern (MID)

AF:

0.517

AC:

151

AN:

292

European-Non Finnish (NFE)

AF:

0.632

AC:

42862

AN:

67848

Other (OTH)

AF:

0.509

AC:

1076

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1740

3480

5220

6960

8700

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

666

1332

1998

2664

3330

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.558

Hom.:

4639

Bravo

AF:

0.470

Asia WGS

AF:

0.541

AC:

1881

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

3.4

(source)

DANN

Benign

0.62

PhyloP100

0.17

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over