17-51747669-CGA-AGC

Variant names:

• chr17-51747669-CGA-AGC
• NM_020178.5:c.427_429delTCGinsGCT
• CA10 p.Ser143Ala

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 1P and 0B. PP3

The NM_020178.5(CA10):​c.427_429delTCGinsGCT​(p.Ser143Ala) 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. S143T) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: CA10 NM_020178.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 9.96
• Publications: 0 publications found

Genes affected

CA10 (HGNC:1369): (carbonic anhydrase 10) This gene encodes a protein that belongs to the carbonic anhydrase family of zinc metalloenzymes, which catalyze the reversible hydration of carbon dioxide in various biological processes. The protein encoded by this gene is an acatalytic member of the alpha-carbonic anhydrase subgroup, and it is thought to play a role in the central nervous system, especially in brain development. Multiple transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PP3: No computational evidence supports a deleterious effect, but strongly conserved according to phyloP

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020178.5. 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
	CA10	NM_020178.5	MANE Select	c.427_429delTCGinsGCT	p.Ser143Ala	missense	N/A	NP_064563.1	A0A384MTY8
	CA10	NM_001082533.1		c.427_429delTCGinsGCT	p.Ser143Ala	missense	N/A	NP_001076002.1	Q9NS85-1
	CA10	NM_001082534.2		c.427_429delTCGinsGCT	p.Ser143Ala	missense	N/A	NP_001076003.1	A0A384MTY8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CA10	ENST00000451037.7	TSL:1 MANE Select	c.427_429delTCGinsGCT	p.Ser143Ala	missense	N/A	ENSP00000405388.2	Q9NS85-1
	CA10	ENST00000285273.8	TSL:1	c.427_429delTCGinsGCT	p.Ser143Ala	missense	N/A	ENSP00000285273.4	Q9NS85-1
	CA10	ENST00000442502.6	TSL:1	c.427_429delTCGinsGCT	p.Ser143Ala	missense	N/A	ENSP00000390666.2	Q9NS85-1

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		10

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: chr17-49825029;