2-96546956-C-T

Variant names:

• chr2-96546956-C-T
• rs2278563
• NM_212481.3:c.5-446C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_212481.3(ARID5A):​c.5-446C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 152,078 control chromosomes in the GnomAD database, including 5,892 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 0.24 (5892 hom., cov: 32)
• Consequence: ARID5A NM_212481.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.102
• Publications: 16 publications found

Genes affected

ARID5A (HGNC:17361): (AT-rich interaction domain 5A) Members of the ARID protein family, including ARID5A, have diverse functions but all appear to play important roles in development, tissue-specific gene expression, and regulation of cell growth (Patsialou et al., 2005 [PubMed 15640446]).[supplied by OMIM, Mar 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.63 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARID5A	NM_212481.3	c.5-446C>T		intron_variant	Intron 1 of 6	ENST00000357485.8	NP_997646.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARID5A	ENST00000357485.8	c.5-446C>T		intron_variant	Intron 1 of 6	1	NM_212481.3	ENSP00000350078.3

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36480 AN: 151960 Hom.: 5878 Cov.: 32

Gnomad AFR AF: 0.0846

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.240 AC: 36510 AN: 152078 Hom.: 5892 Cov.: 32 AF XY: 0.246 AC XY: 18288 AN XY: 74338

African (AFR) AF: 0.0845 AC: 3506 AN: 41500

American (AMR) AF: 0.402 AC: 6135 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1074 AN: 3472

East Asian (EAS) AF: 0.438 AC: 2257 AN: 5158

South Asian (SAS) AF: 0.649 AC: 3131 AN: 4824

European-Finnish (FIN) AF: 0.183 AC: 1937 AN: 10570

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.258 AC: 17546 AN: 67960

Other (OTH) AF: 0.299 AC: 630 AN: 2110

Alfa AF: 0.259 Hom.: 15867

Bravo AF: 0.247

Asia WGS AF: 0.550 AC: 1906 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.8
DANN	Benign	0.81
PhyloP100		-0.10
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: rs2278563; hg19: chr2-97212693;