19-5914940-CCC-GCG

Variant names:

• chr19-5914940-CCC-GCG
• NM_004058.5:c.262_264delCCCinsGCG
• CAPS p.Pro88Ala

Variant summary

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

The NM_004058.5(CAPS):​c.262_264delCCCinsGCG​(p.Pro88Ala) variant causes a missense, splice region change. 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. P88T) has been classified as Benign.

• Frequency: Genomes: not found (cov: 33)
• Consequence: CAPS NM_004058.5 missense, splice_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.94
• Publications: 0 publications found

Genes affected

CAPS (HGNC:1487): (calcyphosine) This gene encodes a calcium-binding protein, which may play a role in the regulation of ion transport. A similar protein was first described as a potentially important regulatory protein in the dog thyroid and was termed as R2D5 antigen in rabbit. Alternative splicing of this gene generates two transcript variants. [provided by RefSeq, Jul 2008]

ENSG00000267571 (HGNC:):

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004058.5. 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
	CAPS	NM_004058.5	MANE Select	c.262_264delCCCinsGCG	p.Pro88Ala	missense splice_region	N/A	NP_004049.3	Q13938-4
	CAPS	NM_080590.4		c.262_264delCCCinsGCG	p.Pro88Ala	missense splice_region	N/A	NP_542157.3	A0A499FJ41

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAPS	ENST00000588776.8	TSL:1 MANE Select	c.262_264delCCCinsGCG	p.Pro88Ala	missense splice_region	N/A	ENSP00000465883.2	Q13938-4
	CAPS	ENST00000585541.1	TSL:1	n.594_596delCCCinsGCG		non_coding_transcript_exon	Exon 2 of 2
	CAPS	ENST00000961097.1		c.262_264delCCCinsGCG	p.Pro88Ala	missense splice_region	N/A	ENSP00000631156.1

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		6.9

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: chr19-5914951;