chr2-96552630-A-G

Variant names:

• chr2-96552630-A-G
• rs6576973
• NM_212481.3:c.*317A>G

Variant summary

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

The NM_212481.3(ARID5A):​c.*317A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0458 in 1,388,782 control chromosomes in the GnomAD database, including 3,696 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 0.10 (1719 hom., cov: 33)
  • Exomes 𝑓: 0.039 (1977 hom.)
• Consequence: ARID5A NM_212481.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.167
• Publications: 14 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_212481.3. 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
	ARID5A	NM_212481.3	MANE Select	c.*317A>G		3_prime_UTR	Exon 7 of 7	NP_997646.1	Q03989-1
	ARID5A	NM_001319085.2		c.*317A>G		3_prime_UTR	Exon 7 of 7	NP_001306014.1
	ARID5A	NM_001319087.2		c.*317A>G		3_prime_UTR	Exon 7 of 7	NP_001306016.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARID5A	ENST00000357485.8	TSL:1 MANE Select	c.*317A>G		3_prime_UTR	Exon 7 of 7	ENSP00000350078.3	Q03989-1
	ARID5A	ENST00000454558.3	TSL:1	c.*317A>G		3_prime_UTR	Exon 7 of 7	ENSP00000400785.1	Q03989-5
	ARID5A	ENST00000412735.5	TSL:1	n.*1786A>G		splice_region non_coding_transcript_exon	Exon 6 of 6	ENSP00000397286.1	F6Q9D3

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15285 AN: 152174 Hom.: 1712 Cov.: 33

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0644

Gnomad ASJ AF: 0.0308

Gnomad EAS AF: 0.0352

Gnomad SAS AF: 0.0445

Gnomad FIN AF: 0.0153

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0302

Gnomad OTH AF: 0.0789

GnomAD2 exomes AF: 0.0543 AC: 4603 AN: 84786 AF XY: 0.0504

Gnomad AFR exome AF: 0.280

Gnomad AMR exome AF: 0.0558

Gnomad ASJ exome AF: 0.0346

Gnomad EAS exome AF: 0.0314

Gnomad FIN exome AF: 0.0149

Gnomad NFE exome AF: 0.0314

Gnomad OTH exome AF: 0.0447

GnomAD4 exome AF: 0.0390 AC: 48243 AN: 1236490 Hom.: 1977 Cov.: 31 AF XY: 0.0385 AC XY: 23178 AN XY: 601508

African (AFR) AF: 0.284 AC: 7930 AN: 27910

American (AMR) AF: 0.0575 AC: 1354 AN: 23562

Ashkenazi Jewish (ASJ) AF: 0.0327 AC: 615 AN: 18814

East Asian (EAS) AF: 0.0192 AC: 537 AN: 27908

South Asian (SAS) AF: 0.0418 AC: 2819 AN: 67446

European-Finnish (FIN) AF: 0.0199 AC: 401 AN: 20132

Middle Eastern (MID) AF: 0.0336 AC: 167 AN: 4970

European-Non Finnish (NFE) AF: 0.0321 AC: 31961 AN: 995370

Other (OTH) AF: 0.0488 AC: 2459 AN: 50378

GnomAD4 genome AF: 0.101 AC: 15332 AN: 152292 Hom.: 1719 Cov.: 33 AF XY: 0.0977 AC XY: 7274 AN XY: 74478

African (AFR) AF: 0.275 AC: 11437 AN: 41514

American (AMR) AF: 0.0645 AC: 988 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0308 AC: 107 AN: 3472

East Asian (EAS) AF: 0.0353 AC: 183 AN: 5180

South Asian (SAS) AF: 0.0439 AC: 212 AN: 4832

European-Finnish (FIN) AF: 0.0153 AC: 163 AN: 10632

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0302 AC: 2055 AN: 68038

Other (OTH) AF: 0.0777 AC: 164 AN: 2112

Alfa AF: 0.0430 Hom.: 877

Bravo AF: 0.110

Asia WGS AF: 0.0610 AC: 213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.4
DANN	Benign	0.39
PhyloP100		0.17
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: rs6576973; hg19: chr2-97218367;