19-971933-A-G

Variant summary

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

The NM_005224.3(ARID3A):c.1650A>G(p.Gly550=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.73 in 1,578,752 control chromosomes in the GnomAD database, including 425,664 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 0.70 (37247 hom., cov: 29)
  • Exomes 𝑓: 0.73 (388417 hom.)
• Consequence: ARID3A NM_005224.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53

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=-0.92).
• BP7: Synonymous conserved (PhyloP=-1.53 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARID3A	NM_005224.3	c.1650A>G	p.Gly550=	synonymous_variant	9/9	ENST00000263620.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARID3A	ENST00000263620.8	c.1650A>G	p.Gly550=	synonymous_variant	9/9	1	NM_005224.3	P1
ARID3A	ENST00000587532.5	c.894A>G	p.Gly298=	synonymous_variant	6/6	5

Frequencies

GnomAD3 genomes AF: 0.696 AC: 105277 AN: 151222 Hom.: 37243 Cov.: 29

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.862

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.765

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.692

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.766

Gnomad OTH AF: 0.732

GnomAD3 exomes AF: 0.664 AC: 141898 AN: 213822 Hom.: 48567 AF XY: 0.668 AC XY: 79111 AN XY: 118438

Gnomad AFR exome AF: 0.633

Gnomad AMR exome AF: 0.525

Gnomad ASJ exome AF: 0.763

Gnomad EAS exome AF: 0.464

Gnomad SAS exome AF: 0.537

Gnomad FIN exome AF: 0.690

Gnomad NFE exome AF: 0.758

Gnomad OTH exome AF: 0.705

GnomAD4 exome AF: 0.734 AC: 1047258 AN: 1427412 Hom.: 388417 Cov.: 51 AF XY: 0.729 AC XY: 517457 AN XY: 710184

Gnomad4 AFR exome AF: 0.642

Gnomad4 AMR exome AF: 0.534

Gnomad4 ASJ exome AF: 0.768

Gnomad4 EAS exome AF: 0.510

Gnomad4 SAS exome AF: 0.537

Gnomad4 FIN exome AF: 0.697

Gnomad4 NFE exome AF: 0.768

Gnomad4 OTH exome AF: 0.716

GnomAD4 genome AF: 0.696 AC: 105322 AN: 151340 Hom.: 37247 Cov.: 29 AF XY: 0.687 AC XY: 50773 AN XY: 73892

Gnomad4 AFR AF: 0.643

Gnomad4 AMR AF: 0.620

Gnomad4 ASJ AF: 0.765

Gnomad4 EAS AF: 0.493

Gnomad4 SAS AF: 0.532

Gnomad4 FIN AF: 0.692

Gnomad4 NFE AF: 0.766

Gnomad4 OTH AF: 0.733

Alfa AF: 0.594 Hom.: 10307

Bravo AF: 0.696

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.4
Dann	Benign	0.37

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: rs1051504; hg19: chr19-971933; COSMIC: COSV55043132; COSMIC: COSV55043132;