rs12553321

Positions:

• chr9-34627336-C-T

Variant summary

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

The NM_001017363.4(ARID3C):​c.318+361G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0346 in 152,138 control chromosomes in the GnomAD database, including 133 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 0.035 (133 hom., cov: 32)
• Consequence: ARID3C NM_001017363.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.274

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARID3C	NM_001017363.4	c.318+361G>A		intron_variant		ENST00000378909.4
ARID3C	NM_001371945.2	c.318+361G>A		intron_variant
ARID3C	XM_047422781.1	c.768+361G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARID3C	ENST00000378909.4	c.318+361G>A		intron_variant		2	NM_001017363.4	P2
ARID3C	ENST00000692051.1	c.318+361G>A		intron_variant				A2

Frequencies

GnomAD3 genomes AF: 0.0346 AC: 5260 AN: 152020 Hom.: 134 Cov.: 32

Gnomad AFR AF: 0.0146

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0268

Gnomad ASJ AF: 0.0778

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.0434

Gnomad MID AF: 0.0513

Gnomad NFE AF: 0.0419

Gnomad OTH AF: 0.0402

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

GnomAD4 genome AF: 0.0346 AC: 5258 AN: 152138 Hom.: 133 Cov.: 32 AF XY: 0.0352 AC XY: 2620 AN XY: 74378

Gnomad4 AFR AF: 0.0146

Gnomad4 AMR AF: 0.0267

Gnomad4 ASJ AF: 0.0778

Gnomad4 EAS AF: 0.00136

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.0434

Gnomad4 NFE AF: 0.0419

Gnomad4 OTH AF: 0.0393

Alfa AF: 0.0422 Hom.: 136

Bravo AF: 0.0302

Asia WGS AF: 0.0440 AC: 155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.9
DANN	Benign	0.49

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: rs12553321; hg19: chr9-34627333;