ENST00000412735.5:n.*1786A>G – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000412735.5(ARID5A):n.*1786A>G variant causes a splice region, non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0458 in 1,388,782 control chromosomes in the GnomAD database, including 3,696 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.10 ( 1719 hom., cov: 33)

Exomes 𝑓: 0.039 ( 1977 hom. )

Consequence

ARID5A
ENST00000412735.5 splice_region, non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.167

Publications

14 publications found

Variant links:

Genes affected

ARID5A (HGNC:17361): (AT-rich interaction domain 5A) Members of the ARID protein family, including ARID5A, have diverse functions but all appear to play important roles in development, tissue-specific gene expression, and regulation of cell growth (Patsialou et al., 2005 [PubMed 15640446]).[supplied by OMIM, Mar 2008]

ARID5A links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

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

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARID5A	NM_212481.3 link	c.*317A>G		3_prime_UTR_variant	Exon 7 of 7	ENST00000357485.8	NP_997646.1	Q03989-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARID5A	ENST00000357485.8 link	c.*317A>G		3_prime_UTR_variant	Exon 7 of 7	1	NM_212481.3	ENSP00000350078.3		Q03989-1

Frequencies

GnomAD3 genomes

AF:

0.100

AC:

15285

AN:

152174

Hom.:

1712

Cov.:

show subpopulations

Gnomad AFR

AF:

0.275

Gnomad AMI

AF:

0.0197

Gnomad AMR

AF:

0.0644

Gnomad ASJ

AF:

0.0308

Gnomad EAS

AF:

0.0352

Gnomad SAS

AF:

0.0445

Gnomad FIN

AF:

0.0153

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.0302

Gnomad OTH

AF:

0.0789

GnomAD2 exomes

AF:

0.0543

AC:

4603

AN:

84786

AF XY:

0.0504

show subpopulations

Gnomad AFR exome

AF:

0.280

Gnomad AMR exome

AF:

0.0558

Gnomad ASJ exome

AF:

0.0346

Gnomad EAS exome

AF:

0.0314

Gnomad FIN exome

AF:

0.0149

Gnomad NFE exome

AF:

0.0314

Gnomad OTH exome

AF:

0.0447

GnomAD4 exome

AF:

0.0390

AC:

48243

AN:

1236490

Hom.:

1977

Cov.:

AF XY:

0.0385

AC XY:

23178

AN XY:

601508

show subpopulations

African (AFR)

AF:

0.284

AC:

7930

AN:

27910

American (AMR)

AF:

0.0575

AC:

1354

AN:

23562

Ashkenazi Jewish (ASJ)

AF:

0.0327

AC:

615

AN:

18814

East Asian (EAS)

AF:

0.0192

AC:

537

AN:

27908

South Asian (SAS)

AF:

0.0418

AC:

2819

AN:

67446

European-Finnish (FIN)

AF:

0.0199

AC:

401

AN:

20132

Middle Eastern (MID)

AF:

0.0336

AC:

167

AN:

4970

European-Non Finnish (NFE)

AF:

0.0321

AC:

31961

AN:

995370

Other (OTH)

AF:

0.0488

AC:

2459

AN:

50378

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.471

Heterozygous variant carriers

2140

4280

6420

8560

10700

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1470

2940

4410

5880

7350

<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:

0.101

AC:

15332

AN:

152292

Hom.:

1719

Cov.:

AF XY:

0.0977

AC XY:

7274

AN XY:

74478

show subpopulations

African (AFR)

AF:

0.275

AC:

11437

AN:

41514

American (AMR)

AF:

0.0645

AC:

988

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.0308

AC:

107

AN:

3472

East Asian (EAS)

AF:

0.0353

AC:

183

AN:

5180

South Asian (SAS)

AF:

0.0439

AC:

212

AN:

4832

European-Finnish (FIN)

AF:

0.0153

AC:

163

AN:

10632

Middle Eastern (MID)

AF:

0.0170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0302

AC:

2055

AN:

68038

Other (OTH)

AF:

0.0777

AC:

164

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

631

1262

1893

2524

3155

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

150

300

450

600

750

<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:

0.0430

Hom.:

877

Bravo

AF:

0.110

Asia WGS

AF:

0.0610

AC:

213

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

2.4

(source)

DANN

Benign

0.39

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