rs71180116
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Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP3
The NM_001388492.1(HTT):c.69_110del(p.Gln25_Gln38del) variant causes a inframe deletion change. The variant allele was found at a frequency of 0.00000516 in 1,357,668 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000076 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0000049 ( 0 hom. )
Consequence
HTT
NM_001388492.1 inframe_deletion
NM_001388492.1 inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.65
Genes affected
HTT (HGNC:4851): (huntingtin) Huntingtin is a disease gene linked to Huntington's disease, a neurodegenerative disorder characterized by loss of striatal neurons. This is thought to be caused by an expanded, unstable trinucleotide repeat in the huntingtin gene, which translates as a polyglutamine repeat in the protein product. A fairly broad range of trinucleotide repeats (9-35) has been identified in normal controls, and repeat numbers in excess of 40 have been described as pathological. The huntingtin locus is large, spanning 180 kb and consisting of 67 exons. The huntingtin gene is widely expressed and is required for normal development. It is expressed as 2 alternatively polyadenylated forms displaying different relative abundance in various fetal and adult tissues. The larger transcript is approximately 13.7 kb and is expressed predominantly in adult and fetal brain whereas the smaller transcript of approximately 10.3 kb is more widely expressed. The genetic defect leading to Huntington's disease may not necessarily eliminate transcription, but may confer a new property on the mRNA or alter the function of the protein. One candidate is the huntingtin-associated protein-1, highly expressed in brain, which has increased affinity for huntingtin protein with expanded polyglutamine repeats. This gene contains an upstream open reading frame in the 5' UTR that inhibits expression of the huntingtin gene product through translational repression. [provided by RefSeq, Jul 2016]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -1 ACMG points.
BP3
?
Nonframeshift variant in repetitive region in NM_001388492.1
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
|---|---|---|---|---|---|---|---|
| HTT | NM_001388492.1 | c.69_110del | p.Gln25_Gln38del | inframe_deletion | 1/67 | ENST00000355072.11 | |
| HTT | NM_002111.8 | c.69_110del | p.Gln27_Gln40del | inframe_deletion | 1/67 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| HTT | ENST00000355072.11 | c.69_110del | p.Gln25_Gln38del | inframe_deletion | 1/67 | 1 | NM_001388492.1 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000759 AC: 1AN: 131786Hom.: 0 Cov.: 0
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GnomAD4 exome AF: 0.00000489 AC: 6AN: 1225882Hom.: 0 AF XY: 0.00000329 AC XY: 2AN XY: 608160
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at