1-8958967-CCG-AGA

Variant names:

• chr1-8958967-CCG-AGA
• NM_001215.4:c.466_468delCCGinsAGA
• CA6 p.Pro156Arg

Variant summary

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

The NM_001215.4(CA6):​c.466_468delCCGinsAGA​(p.Pro156Arg) 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P156T) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CA6 NM_001215.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.09
• Publications: 0 publications found

Genes affected

CA6 (HGNC:1380): (carbonic anhydrase 6) The protein encoded by this gene is one of several isozymes of carbonic anhydrase. This protein is found only in salivary glands and saliva and protein may play a role in the reversible hydratation of carbon dioxide though its function in saliva is unknown. [provided by RefSeq, Jul 2008]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001215.4. 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
	CA6	NM_001215.4	MANE Select	c.466_468delCCGinsAGA	p.Pro156Arg	missense	N/A	NP_001206.2	P23280-1
	CA6	NM_001270500.2		c.466_468delCCGinsAGA	p.Pro156Arg	missense	N/A	NP_001257429.1	P23280-2
	CA6	NM_001270501.2		c.286_288delCCGinsAGA	p.Pro96Arg	missense	N/A	NP_001257430.1	P23280-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CA6	ENST00000377443.7	TSL:1 MANE Select	c.466_468delCCGinsAGA	p.Pro156Arg	missense	N/A	ENSP00000366662.2	P23280-1
	CA6	ENST00000377436.6	TSL:1	c.466_468delCCGinsAGA	p.Pro156Arg	missense	N/A	ENSP00000366654.3	P23280-2
	CA6	ENST00000377442.3	TSL:1	c.286_288delCCGinsAGA	p.Pro96Arg	missense	N/A	ENSP00000366661.2	P23280-3

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		2.1

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: chr1-9019026;