17-80994696-TGGGGCCCGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGGGGGGCCCGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGG-TGGGGCCCGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGG

Variant summary

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

The ENST00000325167.9(CHMP6):​c.173+7_173+45delGGGGCCCGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGG 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
ENST00000325167.9 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.18
Variant links:
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]

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ACMG classification

Classification made for transcript

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 Protein UniProt
CHMP6NM_024591.5 linkc.174-81_174-43delGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGGGGGGCCC intron_variant ENST00000325167.9 NP_078867.2 Q96FZ7
CHMP6XM_005257668.1 linkc.174-81_174-43delGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGGGGGGCCC intron_variant XP_005257725.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CHMP6ENST00000325167.9 linkc.173+7_173+45delGGGGCCCGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGG splice_region_variant, intron_variant 1 NM_024591.5 ENSP00000317468.5 Q96FZ7
CHMP6ENST00000572778.5 linkc.110+7_110+45delGGGGCCCGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGG splice_region_variant, intron_variant 2 ENSP00000461098.1 I3L4A1
CHMP6ENST00000571457.1 linkc.47+7_47+45delGGGGCCCGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGG splice_region_variant, intron_variant 3 ENSP00000461238.1 I3L4G8
CHMP6ENST00000572525.5 linkc.-86+7_-86+45delGGGGCCCGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGG splice_region_variant, intron_variant 3 ENSP00000460389.1 I3L3E4

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

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs71166116; hg19: chr17-78968496; API