1-224617190-GCT-TCA

Variant names:

• chr1-224617190-GCT-TCA
• NM_152495.2:c.16_18delGCTinsTCA
• CNIH3 p.Ala6Ser

Variant summary

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

The NM_152495.2(CNIH3):​c.16_18delGCTinsTCA​(p.Ala6Ser) variant causes a missense change involving the alteration of a 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A6T) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: CNIH3 NM_152495.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.29
• Publications: 0 publications found

Genes affected

CNIH3 (HGNC:26802): (cornichon family AMPA receptor auxiliary protein 3) Predicted to enable channel regulator activity. Involved in regulation of AMPA receptor activity. Predicted to be located in dendritic shaft and postsynaptic membrane. Predicted to be part of AMPA glutamate receptor complex. Predicted to be active in dendrite and glutamatergic synapse. [provided by Alliance of Genome Resources, Apr 2022]

CNIH3-AS2 (HGNC:41162): (CNIH3 antisense RNA 2)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152495.2. 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
	CNIH3	NM_152495.2	MANE Select	c.16_18delGCTinsTCA	p.Ala6Ser	missense	N/A	NP_689708.1	Q8TBE1
	CNIH3	NM_001322305.2		c.16_18delGCTinsTCA	p.Ala6Ser	missense	N/A	NP_001309234.1
	CNIH3	NM_001322302.2		c.166-63768_166-63766delGCTinsTCA		intron	N/A	NP_001309231.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNIH3	ENST00000272133.4	TSL:1 MANE Select	c.16_18delGCTinsTCA	p.Ala6Ser	missense	N/A	ENSP00000272133.3	Q8TBE1
	CNIH3	ENST00000860910.1		c.16_18delGCTinsTCA	p.Ala6Ser	missense	N/A	ENSP00000530969.1
	CNIH3	ENST00000933029.1		c.16_18delGCTinsTCA	p.Ala6Ser	missense	N/A	ENSP00000603088.1

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		7.3

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: chr1-224804892;