rs13283357

Positions:

• chr9-34627943-C-T

Variant summary

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

The NM_001017363.4(ARID3C):​c.72G>A​(p.Pro24=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.331 in 1,551,502 control chromosomes in the GnomAD database, including 91,190 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 0.28 (6821 hom., cov: 33)
  • Exomes 𝑓: 0.34 (84369 hom.)
• Consequence: ARID3C NM_001017363.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00300

Genes affected

ARID3C (HGNC:21209): (AT-rich interaction domain 3C) This gene is a member of the ARID (AT-rich interaction domain) family of proteins. The ARID domain is a helix-turn-helix motif-based DNA-binding domain. 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 -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP7: Synonymous conserved (PhyloP=0.003 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARID3C	NM_001017363.4	c.72G>A	p.Pro24=	synonymous_variant	2/8	ENST00000378909.4
ARID3C	NM_001371945.2	c.72G>A	p.Pro24=	synonymous_variant	2/7
ARID3C	XM_047422781.1	c.522G>A	p.Pro174=	synonymous_variant	3/9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARID3C	ENST00000378909.4	c.72G>A	p.Pro24=	synonymous_variant	2/8	2	NM_001017363.4	P2
ARID3C	ENST00000692051.1	c.72G>A	p.Pro24=	synonymous_variant	2/6			A2

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42190 AN: 152064 Hom.: 6818 Cov.: 33

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.0555

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.312

GnomAD3 exomes AF: 0.279 AC: 42582 AN: 152848 Hom.: 6899 AF XY: 0.277 AC XY: 22628 AN XY: 81716

Gnomad AFR exome AF: 0.148

Gnomad AMR exome AF: 0.253

Gnomad ASJ exome AF: 0.415

Gnomad EAS exome AF: 0.0545

Gnomad SAS exome AF: 0.162

Gnomad FIN exome AF: 0.284

Gnomad NFE exome AF: 0.373

Gnomad OTH exome AF: 0.337

GnomAD4 exome AF: 0.337 AC: 471554 AN: 1399320 Hom.: 84369 Cov.: 36 AF XY: 0.333 AC XY: 230092 AN XY: 690302

Gnomad4 AFR exome AF: 0.148

Gnomad4 AMR exome AF: 0.264

Gnomad4 ASJ exome AF: 0.418

Gnomad4 EAS exome AF: 0.0490

Gnomad4 SAS exome AF: 0.163

Gnomad4 FIN exome AF: 0.290

Gnomad4 NFE exome AF: 0.368

Gnomad4 OTH exome AF: 0.322

GnomAD4 genome AF: 0.277 AC: 42208 AN: 152182 Hom.: 6821 Cov.: 33 AF XY: 0.270 AC XY: 20083 AN XY: 74416

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.420

Gnomad4 EAS AF: 0.0554

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.369

Gnomad4 OTH AF: 0.308

Alfa AF: 0.350 Hom.: 3167

Bravo AF: 0.278

Asia WGS AF: 0.127 AC: 443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.94
DANN	Benign	0.38

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: rs13283357; hg19: chr9-34627940; COSMIC: COSV66698350;