GeneBe

rs71180116

Positions:

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP3

The NM_001388492.1(HTT):​c.69_110delGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA​(p.Gln24_Gln37del) variant causes a disruptive 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 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.65
Variant links:
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]

Genome browser will be placed here

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 Protein UniProt
HTTNM_001388492.1 linkuse as main transcriptc.69_110delGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA p.Gln24_Gln37del disruptive_inframe_deletion 1/67 ENST00000355072.11 NP_001375421.1
HTTNM_002111.8 linkuse as main transcriptc.69_110delGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA p.Gln24_Gln37del disruptive_inframe_deletion 1/67 NP_002102.4 P42858

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
HTTENST00000355072.11 linkuse as main transcriptc.69_110delGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA p.Gln24_Gln37del disruptive_inframe_deletion 1/671 NM_001388492.1 ENSP00000347184.5 P42858

Frequencies

GnomAD3 genomes
AF:
0.00000759
AC:
1
AN:
131786
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.0000282
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.00000489
AC:
6
AN:
1225882
Hom.:
0
AF XY:
0.00000329
AC XY:
2
AN XY:
608160
show subpopulations
Gnomad4 AFR exome
AF:
0.0000387
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000138
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000418
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.00000759
AC:
1
AN:
131786
Hom.:
0
Cov.:
0
AF XY:
0.0000158
AC XY:
1
AN XY:
63316
show subpopulations
Gnomad4 AFR
AF:
0.0000282
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00

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: rs71180116; hg19: chr4-3076603; API