19-965043-T-C

Position:

• chr19-965043-T-C

Variant summary

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

The NM_005224.3(ARID3A):​c.1161T>C​(p.Asn387Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.969 in 1,613,254 control chromosomes in the GnomAD database, including 758,424 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 0.95 (68358 hom., cov: 31)
  • Exomes 𝑓: 0.97 (690066 hom.)
• Consequence: ARID3A NM_005224.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.160

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]

ARID3A (HGNC:):

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BP7: Synonymous conserved (PhyloP=-0.16 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARID3A	NM_005224.3	c.1161T>C	p.Asn387Asn	synonymous_variant	6/9	ENST00000263620.8	NP_005215.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARID3A	ENST00000263620.8	c.1161T>C	p.Asn387Asn	synonymous_variant	6/9	1	NM_005224.3	ENSP00000263620.2
ARID3A	ENST00000587532.5	c.702T>C	p.Asn234Asn	synonymous_variant	4/6	5		ENSP00000464969.3
ARID3A	ENST00000585733.2	n.354T>C		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.947 AC: 143978 AN: 152084 Hom.: 68316 Cov.: 31

Gnomad AFR AF: 0.890

Gnomad AMI AF: 0.955

Gnomad AMR AF: 0.901

Gnomad ASJ AF: 0.981

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.958

Gnomad FIN AF: 0.996

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.977

Gnomad OTH AF: 0.957

GnomAD3 exomes AF: 0.956 AC: 237444 AN: 248380 Hom.: 113780 AF XY: 0.960 AC XY: 129237 AN XY: 134600

Gnomad AFR exome AF: 0.889

Gnomad AMR exome AF: 0.863

Gnomad ASJ exome AF: 0.980

Gnomad EAS exome AF: 1.00

Gnomad SAS exome AF: 0.956

Gnomad FIN exome AF: 0.995

Gnomad NFE exome AF: 0.977

Gnomad OTH exome AF: 0.963

GnomAD4 exome AF: 0.972 AC: 1419474 AN: 1461052 Hom.: 690066 Cov.: 74 AF XY: 0.972 AC XY: 706287 AN XY: 726842

Gnomad4 AFR exome AF: 0.888

Gnomad4 AMR exome AF: 0.869

Gnomad4 ASJ exome AF: 0.980

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.957

Gnomad4 FIN exome AF: 0.994

Gnomad4 NFE exome AF: 0.977

Gnomad4 OTH exome AF: 0.969

GnomAD4 genome AF: 0.947 AC: 144075 AN: 152202 Hom.: 68358 Cov.: 31 AF XY: 0.947 AC XY: 70452 AN XY: 74416

Gnomad4 AFR AF: 0.890

Gnomad4 AMR AF: 0.900

Gnomad4 ASJ AF: 0.981

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.959

Gnomad4 FIN AF: 0.996

Gnomad4 NFE AF: 0.977

Gnomad4 OTH AF: 0.958

Alfa AF: 0.969 Hom.: 30022

Bravo AF: 0.937

Asia WGS AF: 0.981 AC: 3411 AN: 3478

EpiCase AF: 0.975

EpiControl AF: 0.974

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	0.082
DANN	Benign	0.36
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7

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: rs12608658; hg19: chr19-965043;