9-34622392-A-T

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001017363.4(ARID3C):​c.1003T>A​(p.Cys335Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/22 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: not found (cov: 33)
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.035937756).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARID3C	NM_001017363.4	c.1003T>A	p.Cys335Ser	missense_variant	Exon 6 of 8	ENST00000378909.4	NP_001017363.1
ARID3C	XM_047422781.1	c.1453T>A	p.Cys485Ser	missense_variant	Exon 7 of 9		XP_047278737.1
ARID3C	NM_001371945.2	c.866-283T>A		intron_variant	Intron 5 of 6		NP_001358874.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARID3C	ENST00000378909.4	c.1003T>A	p.Cys335Ser	missense_variant	Exon 6 of 8	2	NM_001017363.4	ENSP00000368189.2
ARID3C	ENST00000692051.1	c.866-283T>A		intron_variant	Intron 5 of 5			ENSP00000510553.1
ENSG00000294750	ENST00000725698.1	n.647-204A>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 74

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.060
BayesDel_addAF	Benign	-0.35	T
BayesDel_noAF	Benign	-0.75
CADD	Benign	13
DANN	Benign	0.78
DEOGEN2	Benign	0.0012	T
Eigen	Benign	-1.3
Eigen_PC	Benign	-1.2
FATHMM_MKL	Benign	0.0076	N
LIST_S2	Benign	0.15	T
M_CAP	Benign	0.0030	T
MetaRNN	Benign	0.036	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.69	N
PhyloP100		-0.052
PrimateAI	Benign	0.32	T
PROVEAN	Benign	0.56	N
REVEL	Benign	0.021
Sift	Benign	0.43	T
Sift4G	Benign	0.44	T
Polyphen		0.0010	B
Vest4		0.037
MutPred		0.20		Gain of phosphorylation at C335 (P = 0.0011);
MVP		0.067
MPC		0.31
ClinPred		0.15	T
GERP RS		0.29
Varity_R		0.042
gMVP		0.31
Mutation Taster		=99/1	polymorphism

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;