rs71166116

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr17-80994696-TGGGGCCCGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGGGGGGCCCGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGG-T
• chr17-80994696-TGGGGCCCGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGGGGGGCCCGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGG-TGGGGCCCGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGG

Variant summary

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

The NM_024591.5(CHMP6):​c.174-120_174-43delGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGGGGGGCCCGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGGGGGGCCC variant causes a 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 NM_024591.5 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHMP6	NM_024591.5	c.174-120_174-43delGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGGGGGGCCCGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGGGGGGCCC		intron_variant	Intron 2 of 7	ENST00000325167.9	NP_078867.2
CHMP6	XM_005257668.1	c.174-120_174-43delGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGGGGGGCCCGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGGGGGGCCC		intron_variant	Intron 2 of 6		XP_005257725.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHMP6	ENST00000325167.9	c.173+7_173+84delGGGGCCCGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGGGGGGCCCGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGG		splice_region_variant, intron_variant	Intron 2 of 7	1	NM_024591.5	ENSP00000317468.5
CHMP6	ENST00000572778.5	c.110+7_110+84delGGGGCCCGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGGGGGGCCCGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGG		splice_region_variant, intron_variant	Intron 1 of 5	2		ENSP00000461098.1
CHMP6	ENST00000571457.1	c.47+7_47+84delGGGGCCCGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGGGGGGCCCGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGG		splice_region_variant, intron_variant	Intron 1 of 6	3		ENSP00000461238.1
CHMP6	ENST00000572525.5	c.-86+7_-86+84delGGGGCCCGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGGGGGGCCCGGGCAGCGTGGGCACCCTGTCGGCTGGGGTGG		splice_region_variant, intron_variant	Intron 2 of 7	3		ENSP00000460389.1

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
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;