rs3826948

Positions:

• chr19-929678-G-A

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.174

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
ARID3A	NM_005224.3	c.150G>A	p.Glu50Glu	synonymous_variant	2/9	ENST00000263620.8	NP_005215.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARID3A	ENST00000263620.8	c.150G>A	p.Glu50Glu	synonymous_variant	2/9	1	NM_005224.3	ENSP00000263620.2

Frequencies

GnomAD3 genomes AF: 0.493 AC: 74798 AN: 151864 Hom.: 21255 Cov.: 33

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

GnomAD3 exomes AF: 0.553 AC: 88687 AN: 160280 Hom.: 25643 AF XY: 0.558 AC XY: 49423 AN XY: 88564

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 SAS exome AF: 0.514

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.: 73 AF XY: 0.607 AC XY: 421802 AN XY: 694922

Gnomad4 AFR exome AF: 0.172

Gnomad4 AMR exome AF: 0.478

Gnomad4 ASJ exome AF: 0.562

Gnomad4 EAS exome AF: 0.636

Gnomad4 SAS exome AF: 0.524

Gnomad4 FIN exome AF: 0.632

Gnomad4 NFE exome AF: 0.633

Gnomad4 OTH exome AF: 0.587

GnomAD4 genome AF: 0.492 AC: 74801 AN: 151976 Hom.: 21254 Cov.: 33 AF XY: 0.494 AC XY: 36720 AN XY: 74300

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.497

Gnomad4 ASJ AF: 0.551

Gnomad4 EAS AF: 0.642

Gnomad4 SAS AF: 0.543

Gnomad4 FIN AF: 0.633

Gnomad4 NFE AF: 0.632

Gnomad4 OTH AF: 0.509

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
DANN	Benign	0.62

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

Other links and lift over

dbSNP: rs3826948; hg19: chr19-929678; COSMIC: COSV55043754; COSMIC: COSV55043754;