19-929753-A-G

Variant names:

• chr19-929753-A-G
• rs1799595
• NM_005224.3:c.225A>G

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The ENST00000263620.8(ARID3A):​c.225A>G​(p.Pro75Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.844 in 1,555,082 control chromosomes in the GnomAD database, including 554,157 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 0.86 (56180 hom., cov: 33)
  • Exomes 𝑓: 0.84 (497977 hom.)
• Consequence: ARID3A ENST00000263620.8 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.64
• Publications: 14 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BP7: Synonymous conserved (PhyloP=-3.64 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000263620.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARID3A	NM_005224.3	MANE Select	c.225A>G	p.Pro75Pro	synonymous	Exon 2 of 9	NP_005215.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARID3A	ENST00000263620.8	TSL:1 MANE Select	c.225A>G	p.Pro75Pro	synonymous	Exon 2 of 9	ENSP00000263620.2

Frequencies

GnomAD3 genomes AF: 0.858 AC: 130504 AN: 152016 Hom.: 56132 Cov.: 33

Gnomad AFR AF: 0.899

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.830

Gnomad ASJ AF: 0.825

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.845

Gnomad FIN AF: 0.834

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.838

Gnomad OTH AF: 0.843

GnomAD2 exomes AF: 0.847 AC: 133950 AN: 158058 AF XY: 0.845

Gnomad AFR exome AF: 0.896

Gnomad AMR exome AF: 0.813

Gnomad ASJ exome AF: 0.825

Gnomad EAS exome AF: 1.00

Gnomad FIN exome AF: 0.836

Gnomad NFE exome AF: 0.838

Gnomad OTH exome AF: 0.833

GnomAD4 exome AF: 0.842 AC: 1181154 AN: 1402948 Hom.: 497977 Cov.: 85 AF XY: 0.841 AC XY: 583668 AN XY: 693934

African (AFR) AF: 0.901 AC: 29282 AN: 32510

American (AMR) AF: 0.819 AC: 30437 AN: 37150

Ashkenazi Jewish (ASJ) AF: 0.826 AC: 20888 AN: 25294

East Asian (EAS) AF: 1.00 AC: 37256 AN: 37272

South Asian (SAS) AF: 0.831 AC: 66973 AN: 80584

European-Finnish (FIN) AF: 0.846 AC: 31528 AN: 37268

Middle Eastern (MID) AF: 0.808 AC: 4202 AN: 5200

European-Non Finnish (NFE) AF: 0.836 AC: 910784 AN: 1089210

Other (OTH) AF: 0.852 AC: 49804 AN: 58460

GnomAD4 genome AF: 0.859 AC: 130609 AN: 152134 Hom.: 56180 Cov.: 33 AF XY: 0.858 AC XY: 63855 AN XY: 74388

African (AFR) AF: 0.899 AC: 37314 AN: 41516

American (AMR) AF: 0.830 AC: 12686 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.825 AC: 2863 AN: 3470

East Asian (EAS) AF: 0.998 AC: 5153 AN: 5162

South Asian (SAS) AF: 0.845 AC: 4083 AN: 4830

European-Finnish (FIN) AF: 0.834 AC: 8832 AN: 10592

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.838 AC: 56966 AN: 67954

Other (OTH) AF: 0.845 AC: 1788 AN: 2116

Alfa AF: 0.844 Hom.: 9923

Bravo AF: 0.859

Asia WGS AF: 0.919 AC: 3191 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.036
DANN	Benign	0.29
PhyloP100		-3.6
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1799595; hg19: chr19-929753; COSMIC: COSV55043145; COSMIC: COSV55043145;