9-34622390-GCA-CCT

Variant names:

• chr9-34622390-GCA-CCT
• NM_001017363.4:c.1003_1005delTGCinsAGG
• ARID3C p.Cys335Arg

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001017363.4(ARID3C):​c.1003_1005delTGCinsAGG​(p.Cys335Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ARID3C NM_001017363.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26
• Publications: 0 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: Uncertain_significance. The variant received 0 ACMG points.

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.1003_1005delTGCinsAGG	p.Cys335Arg	missense	N/A	NP_001017363.1	A6NKF2
	ARID3C	NM_001371945.2		c.866-283_866-281delTGCinsAGG		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.1003_1005delTGCinsAGG	p.Cys335Arg	missense	N/A	ENSP00000368189.2	A6NKF2
	ARID3C	ENST00000876981.1		c.866-283_866-281delTGCinsAGG		intron	N/A	ENSP00000547040.1
	ARID3C	ENST00000692051.1		c.866-283_866-281delTGCinsAGG		intron	N/A	ENSP00000510553.1	A0A8I5QL24

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr9-34622387;