Variant rs3808869 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: 𝑓 0.58 ( 26157 hom., cov: 33)

Exomes 𝑓: 0.53 ( 206318 hom. )

Consequence

ARID3C
NM_001017363.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0520

Variant links:

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]

ARID3C links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARID3C	NM_001017363.4 link	c.1003T>G	p.Cys335Gly	missense_variant	6/8	ENST00000378909.4	NP_001017363.1	A6NKF2
ARID3C	XM_047422781.1 link	c.1453T>G	p.Cys485Gly	missense_variant	7/9		XP_047278737.1
ARID3C	NM_001371945.2 link	c.866-283T>G		intron_variant			NP_001358874.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARID3C	ENST00000378909.4 link	c.1003T>G	p.Cys335Gly	missense_variant	6/8	2	NM_001017363.4	ENSP00000368189.2		A6NKF2
ARID3C	ENST00000692051.1 link	c.866-283T>G		intron_variant				ENSP00000510553.1		A0A8I5QL24

Frequencies

GnomAD3 genomes

AF:

0.577

AC:

87726

AN:

151982

Hom.:

26121

Cov.:

show subpopulations

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

GnomAD3 exomes

AF:

0.551

AC:

137601

AN:

249686

Hom.:

39140

AF XY:

0.544

AC XY:

73437

AN XY:

134976

show subpopulations

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 SAS exome

AF:

0.614

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.:

AF XY:

0.529

AC XY:

383979

AN XY:

726378

show subpopulations

Gnomad4 AFR exome

AF:

0.732

Gnomad4 AMR exome

AF:

0.668

Gnomad4 ASJ exome

AF:

0.477

Gnomad4 EAS exome

AF:

0.467

Gnomad4 SAS exome

AF:

0.615

Gnomad4 FIN exome

AF:

0.475

Gnomad4 NFE exome

AF:

0.516

Gnomad4 OTH exome

AF:

0.528

GnomAD4 genome

AF:

0.577

AC:

87805

AN:

152100

Hom.:

26157

Cov.:

AF XY:

0.575

AC XY:

42772

AN XY:

74370

show subpopulations

Gnomad4 AFR

AF:

0.727

Gnomad4 AMR

AF:

0.588

Gnomad4 ASJ

AF:

0.474

Gnomad4 EAS

AF:

0.468

Gnomad4 SAS

AF:

0.608

Gnomad4 FIN

AF:

0.471

Gnomad4 NFE

AF:

0.511

Gnomad4 OTH

AF:

0.547

Alfa

AF:

0.521

Hom.:

33538

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 v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.043

BayesDel_addAF

Benign

-0.80

BayesDel_noAF

Benign

-0.78

CADD

Benign

DANN

Benign

0.71

DEOGEN2

Benign

0.0013

Eigen

Benign

-1.4

Eigen_PC

Benign

-1.2

FATHMM_MKL

Benign

0.00092

LIST_S2

Benign

0.11

MetaRNN

Benign

0.0000013

MetaSVM

Benign

-1.0

MutationAssessor

Benign

-1.4

PrimateAI

Benign

0.31

PROVEAN

Benign

-0.16

REVEL

Benign

0.057

Sift

Benign

0.42

Sift4G

Benign

0.38

Polyphen

0.0

Vest4

0.024

MPC

0.32

ClinPred

0.0026

GERP RS

0.29

Varity_R

0.047

gMVP

0.32

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over