chr9-34622392-A-C

Variant names:

• chr9-34622392-A-C
• rs3808869
• NM_001017363.4:c.1003T>G

Variant summary

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

The NM_001017363.4(ARID3C):​c.1003T>G​(p.Cys335Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.533 in 1,612,312 control chromosomes in the GnomAD database, including 232,475 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.58 (26157 hom., cov: 33)
  • Exomes 𝑓: 0.53 (206318 hom.)
• Consequence: ARID3C NM_001017363.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0520
• Publications: 27 publications found

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]

ENSG00000294750 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (MetaRNN=1.2974782E-6).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001017363.4. 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
	ARID3C	NM_001017363.4	MANE Select	c.1003T>G	p.Cys335Gly	missense	Exon 6 of 8	NP_001017363.1	A6NKF2
	ARID3C	NM_001371945.2		c.866-283T>G		intron	N/A	NP_001358874.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARID3C	ENST00000378909.4	TSL:2 MANE Select	c.1003T>G	p.Cys335Gly	missense	Exon 6 of 8	ENSP00000368189.2	A6NKF2
	ARID3C	ENST00000876981.1		c.866-283T>G		intron	N/A	ENSP00000547040.1
	ARID3C	ENST00000692051.1		c.866-283T>G		intron	N/A	ENSP00000510553.1	A0A8I5QL24

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87726 AN: 151982 Hom.: 26121 Cov.: 33

Gnomad AFR AF: 0.727

Gnomad AMI AF: 0.691

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.552

GnomAD2 exomes AF: 0.551 AC: 137601 AN: 249686 AF XY: 0.544

Gnomad AFR exome AF: 0.729

Gnomad AMR exome AF: 0.683

Gnomad ASJ exome AF: 0.478

Gnomad EAS exome AF: 0.471

Gnomad FIN exome AF: 0.477

Gnomad NFE exome AF: 0.505

Gnomad OTH exome AF: 0.515

GnomAD4 exome AF: 0.528 AC: 771180 AN: 1460212 Hom.: 206318 Cov.: 74 AF XY: 0.529 AC XY: 383979 AN XY: 726378

African (AFR) AF: 0.732 AC: 24398 AN: 33344

American (AMR) AF: 0.668 AC: 29593 AN: 44308

Ashkenazi Jewish (ASJ) AF: 0.477 AC: 12423 AN: 26044

East Asian (EAS) AF: 0.467 AC: 18539 AN: 39696

South Asian (SAS) AF: 0.615 AC: 52912 AN: 86050

European-Finnish (FIN) AF: 0.475 AC: 25357 AN: 53394

Middle Eastern (MID) AF: 0.515 AC: 2960 AN: 5748

European-Non Finnish (NFE) AF: 0.516 AC: 573157 AN: 1111324

Other (OTH) AF: 0.528 AC: 31841 AN: 60304

GnomAD4 genome AF: 0.577 AC: 87805 AN: 152100 Hom.: 26157 Cov.: 33 AF XY: 0.575 AC XY: 42772 AN XY: 74370

African (AFR) AF: 0.727 AC: 30152 AN: 41476

American (AMR) AF: 0.588 AC: 8989 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.474 AC: 1646 AN: 3472

East Asian (EAS) AF: 0.468 AC: 2421 AN: 5168

South Asian (SAS) AF: 0.608 AC: 2927 AN: 4814

European-Finnish (FIN) AF: 0.471 AC: 4982 AN: 10582

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.511 AC: 34749 AN: 67988

Other (OTH) AF: 0.547 AC: 1155 AN: 2110

Alfa AF: 0.529 Hom.: 71994

Bravo AF: 0.591

TwinsUK AF: 0.512 AC: 1898

ALSPAC AF: 0.522 AC: 2012

ESP6500AA AF: 0.727 AC: 3203

ESP6500EA AF: 0.511 AC: 4398

ExAC AF: 0.552 AC: 66979

Asia WGS AF: 0.527 AC: 1833 AN: 3478

EpiCase AF: 0.508

EpiControl AF: 0.496

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.043
BayesDel_addAF	Benign	-0.80	T
BayesDel_noAF	Benign	-0.78
CADD	Benign	12
DANN	Benign	0.71
DEOGEN2	Benign	0.0013	T
Eigen	Benign	-1.4
Eigen_PC	Benign	-1.2
FATHMM_MKL	Benign	0.00092	N
LIST_S2	Benign	0.11	T
MetaRNN	Benign	0.0000013	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	-1.4	N
PhyloP100		-0.052
PrimateAI	Benign	0.31	T
PROVEAN	Benign	-0.16	N
REVEL	Benign	0.057
Sift	Benign	0.42	T
Sift4G	Benign	0.38	T
Polyphen		0.0	B
Vest4		0.024
MPC		0.32
ClinPred		0.0026	T
GERP RS		0.29
Varity_R		0.047
gMVP		0.32
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: rs3808869; hg19: chr9-34622389; COSMIC: COSV52406371; COSMIC: COSV52406371;