19-955577-G-A

Position:

• chr19-955577-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005224.3(ARID3A):​c.694-4515G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.807 in 152,194 control chromosomes in the GnomAD database, including 50,414 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 0.81 (50414 hom., cov: 34)
• Consequence: ARID3A NM_005224.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.398

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.875 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARID3A	NM_005224.3	c.694-4515G>A		intron_variant		ENST00000263620.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARID3A	ENST00000263620.8	c.694-4515G>A		intron_variant		1	NM_005224.3	P1
ARID3A	ENST00000587532.5	c.235-4515G>A		intron_variant		5
ARID3A	ENST00000457152.3	c.179-4515G>A		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.807 AC: 122769 AN: 152076 Hom.: 50396 Cov.: 34

Gnomad AFR AF: 0.760

Gnomad AMI AF: 0.862

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.893

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.816

Gnomad FIN AF: 0.790

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.881

Gnomad OTH AF: 0.835

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.807 AC: 122826 AN: 152194 Hom.: 50414 Cov.: 34 AF XY: 0.800 AC XY: 59522 AN XY: 74400

Gnomad4 AFR AF: 0.760

Gnomad4 AMR AF: 0.693

Gnomad4 ASJ AF: 0.893

Gnomad4 EAS AF: 0.495

Gnomad4 SAS AF: 0.818

Gnomad4 FIN AF: 0.790

Gnomad4 NFE AF: 0.881

Gnomad4 OTH AF: 0.837

Alfa AF: 0.865 Hom.: 34726

Bravo AF: 0.798

Asia WGS AF: 0.678 AC: 2358 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.9
DANN	Benign	0.52

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: rs349313; hg19: chr19-955577;