19-971933-A-G

Variant names:

• chr19-971933-A-G
• rs1051504
• NM_005224.3:c.1650A>G

Variant summary

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

The NM_005224.3(ARID3A):​c.1650A>G​(p.Gly550Gly) 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
• 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=-0.92).
• 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005224.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARID3A	NM_005224.3	MANE Select	c.1650A>G	p.Gly550Gly	synonymous	Exon 9 of 9	NP_005215.1	Q99856

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARID3A	ENST00000263620.8	TSL:1 MANE Select	c.1650A>G	p.Gly550Gly	synonymous	Exon 9 of 9	ENSP00000263620.2	Q99856
	ARID3A	ENST00000852898.1		c.1650A>G	p.Gly550Gly	synonymous	Exon 9 of 9	ENSP00000522957.1
	ARID3A	ENST00000937801.1		c.1650A>G	p.Gly550Gly	synonymous	Exon 9 of 9	ENSP00000607860.1

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

GnomAD2 exomes AF: 0.664 AC: 141898 AN: 213822 AF XY: 0.668

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 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

African (AFR) AF: 0.642 AC: 19855 AN: 30936

American (AMR) AF: 0.534 AC: 21034 AN: 39370

Ashkenazi Jewish (ASJ) AF: 0.768 AC: 19210 AN: 25012

East Asian (EAS) AF: 0.510 AC: 19151 AN: 37546

South Asian (SAS) AF: 0.537 AC: 44740 AN: 83262

European-Finnish (FIN) AF: 0.697 AC: 36277 AN: 52040

Middle Eastern (MID) AF: 0.757 AC: 4179 AN: 5520

European-Non Finnish (NFE) AF: 0.768 AC: 840761 AN: 1094970

Other (OTH) AF: 0.716 AC: 42051 AN: 58756

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

African (AFR) AF: 0.643 AC: 26561 AN: 41326

American (AMR) AF: 0.620 AC: 9414 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.765 AC: 2647 AN: 3458

East Asian (EAS) AF: 0.493 AC: 2521 AN: 5112

South Asian (SAS) AF: 0.532 AC: 2558 AN: 4804

European-Finnish (FIN) AF: 0.692 AC: 7213 AN: 10416

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.766 AC: 51866 AN: 67744

Other (OTH) AF: 0.733 AC: 1530 AN: 2086

Alfa AF: 0.594 Hom.: 10307

Bravo AF: 0.696

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.37
PhyloP100		-1.5
Mutation Taster		=99/1	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: rs1051504; hg19: chr19-971933; COSMIC: COSV55043132; COSMIC: COSV55043132;