9-34623481-G-T

Variant names:

• chr9-34623481-G-T
• rs1346092550
• NM_001017363.4:c.809C>A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001017363.4(ARID3C):​c.809C>A​(p.Thr270Asn) 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. 14/21 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: not found (cov: 31)
• Consequence: ARID3C NM_001017363.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29

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 Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.13091236).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARID3C	NM_001017363.4	c.809C>A	p.Thr270Asn	missense_variant	Exon 5 of 8	ENST00000378909.4	NP_001017363.1
ARID3C	NM_001371945.2	c.809C>A	p.Thr270Asn	missense_variant	Exon 5 of 7		NP_001358874.1
ARID3C	XM_047422781.1	c.1259C>A	p.Thr420Asn	missense_variant	Exon 6 of 9		XP_047278737.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARID3C	ENST00000378909.4	c.809C>A	p.Thr270Asn	missense_variant	Exon 5 of 8	2	NM_001017363.4	ENSP00000368189.2
ARID3C	ENST00000692051.1	c.809C>A	p.Thr270Asn	missense_variant	Exon 5 of 6			ENSP00000510553.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 31

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.079
BayesDel_addAF	Benign	-0.30	T
BayesDel_noAF	Benign	-0.67
CADD	Benign	12
DANN	Benign	0.95
DEOGEN2	Benign	0.0038	T
Eigen	Benign	-0.52
Eigen_PC	Benign	-0.55
FATHMM_MKL	Benign	0.50	D
LIST_S2	Benign	0.17	T
M_CAP	Benign	0.017	T
MetaRNN	Benign	0.13	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.9	L
PrimateAI	Uncertain	0.66	T
PROVEAN	Benign	-0.44	N
REVEL	Benign	0.090
Sift	Benign	0.11	T
Sift4G	Benign	0.22	T
Polyphen		0.73	P
Vest4		0.076
MutPred		0.20		Loss of glycosylation at T270 (P = 0.0046);
MVP		0.081
MPC		0.38
ClinPred		0.10	T
GERP RS		2.4
Varity_R		0.053
gMVP		0.27

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: rs1346092550; hg19: chr9-34623478;