rs7081363
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_024467.1(HECTD2-AS1):n.427-59313C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 151,772 control chromosomes in the GnomAD database, including 6,289 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 0.19 ( 6289 hom., cov: 32)
Exomes 𝑓: 0.043 ( 0 hom. )
Consequence
HECTD2-AS1
NR_024467.1 intron, non_coding_transcript
NR_024467.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0300
Genes affected
HECTD2 (HGNC:26736): (HECT domain E3 ubiquitin protein ligase 2) Predicted to enable ubiquitin-protein transferase activity. Predicted to be involved in protein ubiquitination. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.71).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.531 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HECTD2-AS1 | NR_024467.1 | n.427-59313C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENST00000688440.1 | n.322-59313C>T | intron_variant, non_coding_transcript_variant | |||||||
HECTD2 | ENST00000631422.1 | c.-184+771G>A | intron_variant | 3 | |||||
ENST00000700888.1 | n.219-59313C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.188 AC: 28427AN: 151426Hom.: 6269 Cov.: 32
GnomAD3 genomes
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32
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GnomAD4 exome AF: 0.0431 AC: 10AN: 232Hom.: 0 AF XY: 0.0317 AC XY: 4AN XY: 126
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GnomAD4 genome ? AF: 0.188 AC: 28488AN: 151540Hom.: 6289 Cov.: 32 AF XY: 0.183 AC XY: 13556AN XY: 74094
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at