rs71166116

chr17-80994696-TGGGGCCCGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGGGGGGCCCGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGG-Tchr17-80994696-TGGGGCCCGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGGGGGGCCCGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGG-TGGGGCCCGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGG

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_024591.5(CHMP6):c.174-120_174-43del 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CHMP6 NM_024591.5 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18

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

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHMP6	NM_024591.5	c.174-120_174-43del		splice_region_variant, intron_variant		ENST00000325167.9
CHMP6	XM_005257668.1	c.174-120_174-43del		splice_region_variant, intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHMP6	ENST00000325167.9	c.174-120_174-43del		splice_region_variant, intron_variant		1	NM_024591.5	P1
CHMP6	ENST00000571457.1	c.48-120_48-43del		splice_region_variant, intron_variant		3
CHMP6	ENST00000572525.5	c.-85-120_-85-43del		splice_region_variant, intron_variant		3
CHMP6	ENST00000572778.5	c.111-120_111-43del		splice_region_variant, intron_variant		2

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 v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs71166116; hg19: chr17-78968496;