rs9322817
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_020771.4(HACE1):c.1478+59T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 1,140,862 control chromosomes in the GnomAD database, including 79,259 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 0.42 ( 14207 hom., cov: 31)
Exomes 𝑓: 0.36 ( 65052 hom. )
Consequence
HACE1
NM_020771.4 intron
NM_020771.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.946
Genes affected
HACE1 (HGNC:21033): (HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1) This gene encodes a HECT domain and ankyrin repeat-containing ubiquitin ligase. The encoded protein is involved in specific tagging of target proteins, leading to their subcellular localization or proteasomal degradation. The protein is a potential tumor suppressor and is involved in the pathophysiology of several tumors, including Wilm's tumor. [provided by RefSeq, Mar 2016]
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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 (BayesDel_noAF=-0.84).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.585 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HACE1 | NM_020771.4 | c.1478+59T>G | intron_variant | ENST00000262903.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HACE1 | ENST00000262903.9 | c.1478+59T>G | intron_variant | 1 | NM_020771.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.417 AC: 63375AN: 151798Hom.: 14188 Cov.: 31
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GnomAD4 exome AF: 0.358 AC: 354001AN: 988946Hom.: 65052 Cov.: 13 AF XY: 0.357 AC XY: 183111AN XY: 513542
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GnomAD4 genome ? AF: 0.418 AC: 63449AN: 151916Hom.: 14207 Cov.: 31 AF XY: 0.412 AC XY: 30570AN XY: 74242
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at