chr17-80994696-TGGGGCCCGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGGGGGGCCCGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGG-T

Variant names:

• chr17-80994696-TGGGGCCCGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGGGGGGCCCGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGG-T
• rs71166116
• NM_024591.5:c.174-120_174-43delGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGGGGGGCCCGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGGGGGGCCC

Variant summary

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

The ENST00000325167.9(CHMP6):​c.173+7_173+84delGGGGCCCGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGGGGGGCCCGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGG variant causes a splice region, intron 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 DEL_BIG, 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: CHMP6 ENST00000325167.9 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18
• Publications: 0 publications found

Genes affected

CHMP6 (HGNC:25675): (charged multivesicular body protein 6) This gene encodes a member of the chromatin-modifying protein/charged multivesicular body protein family. Proteins in this family are part of the ESCRT-III (endosomal sorting complex required for transport III) which degrades surface receptors, and in biosynthesis of endosomes. [provided by RefSeq, Mar 2012]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000325167.9. 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
	CHMP6	NM_024591.5	MANE Select	c.174-120_174-43delGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGGGGGGCCCGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGGGGGGCCC		intron	N/A	NP_078867.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHMP6	ENST00000325167.9	TSL:1 MANE Select	c.173+7_173+84delGGGGCCCGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGGGGGGCCCGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGG		splice_region intron	N/A	ENSP00000317468.5	Q96FZ7
	CHMP6	ENST00000572778.5	TSL:2	c.110+7_110+84delGGGGCCCGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGGGGGGCCCGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGG		splice_region intron	N/A	ENSP00000461098.1	I3L4A1
	CHMP6	ENST00000571457.1	TSL:3	c.47+7_47+84delGGGGCCCGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGGGGGGCCCGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGG		splice_region intron	N/A	ENSP00000461238.1	I3L4G8

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		1.2

Splicing

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

Other links and lift over

dbSNP: rs71166116; hg19: chr17-78968496;