Variant rs71166116 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000325167.9(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
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]

CHMP6 links:

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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
CHMP6	NM_024591.5 linkuse as main transcript	c.174-120_174-43del		splice_region_variant, intron_variant		ENST00000325167.9	NP_078867.2
CHMP6	XM_005257668.1 linkuse as main transcript	c.174-120_174-43del		splice_region_variant, intron_variant			XP_005257725.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris
CHMP6	ENST00000325167.9 linkuse as main transcript	c.174-120_174-43del	splice_region_variant, intron_variant	1	NM_024591.5	ENSP00000317468	P1
CHMP6	ENST00000571457.1 linkuse as main transcript	c.48-120_48-43del	splice_region_variant, intron_variant	3		ENSP00000461238
CHMP6	ENST00000572525.5 linkuse as main transcript	c.-85-120_-85-43del	splice_region_variant, intron_variant	3		ENSP00000460389
CHMP6	ENST00000572778.5 linkuse as main transcript	c.111-120_111-43del	splice_region_variant, intron_variant	2		ENSP00000461098

Frequencies

GnomAD3 genomes

Cov.:

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

Cov.:

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.