rs1167796
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005338.7(HIP1):c.2766+834C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 152,046 control chromosomes in the GnomAD database, including 9,624 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.33 ( 9624 hom., cov: 31)
Consequence
HIP1
NM_005338.7 intron
NM_005338.7 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.256
Genes affected
HIP1 (HGNC:4913): (huntingtin interacting protein 1) The product of this gene is a membrane-associated protein that functions in clathrin-mediated endocytosis and protein trafficking within the cell. The encoded protein binds to the huntingtin protein in the brain; this interaction is lost in Huntington's disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (Cadd=0.77).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HIP1 | NM_005338.7 | c.2766+834C>T | intron_variant | ENST00000336926.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HIP1 | ENST00000336926.11 | c.2766+834C>T | intron_variant | 1 | NM_005338.7 | P1 | |||
HIP1 | ENST00000616821.4 | c.2679+834C>T | intron_variant | 1 | |||||
HIP1 | ENST00000434438.6 | c.2613+834C>T | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.327 AC: 49721AN: 151928Hom.: 9632 Cov.: 31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.327 AC: 49710AN: 152046Hom.: 9624 Cov.: 31 AF XY: 0.330 AC XY: 24518AN XY: 74308
GnomAD4 genome
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ClinVar
Not reported inComputational scores
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Prediction
CADD
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at