rs2274201
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1
The NM_015382.4(HECTD1):c.360C>T(p.Ala120=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 1,609,034 control chromosomes in the GnomAD database, including 154,671 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.50 ( 20360 hom., cov: 31)
Exomes 𝑓: 0.42 ( 134311 hom. )
Consequence
HECTD1
NM_015382.4 synonymous
NM_015382.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.405
Genes affected
HECTD1 (HGNC:20157): (HECT domain E3 ubiquitin protein ligase 1) Predicted to enable ubiquitin protein ligase activity. Predicted to be involved in anatomical structure development; positive regulation of proteasomal ubiquitin-dependent protein catabolic process; and protein K63-linked ubiquitination. Predicted to act upstream of or within several processes, including animal organ development; negative regulation of protein localization to plasma membrane; and protein autoubiquitination. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.36).
BP6
?
Variant 14-31178035-G-A is Benign according to our data. Variant chr14-31178035-G-A is described in ClinVar as [Benign]. Clinvar id is 1178217.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.405 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HECTD1 | NM_015382.4 | c.360C>T | p.Ala120= | synonymous_variant | 3/43 | ENST00000399332.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HECTD1 | ENST00000399332.6 | c.360C>T | p.Ala120= | synonymous_variant | 3/43 | 5 | NM_015382.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.502 AC: 76201AN: 151738Hom.: 20313 Cov.: 31
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GnomAD3 exomes AF: 0.473 AC: 117830AN: 249372Hom.: 29141 AF XY: 0.462 AC XY: 62540AN XY: 135304
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GnomAD4 exome AF: 0.423 AC: 616810AN: 1457174Hom.: 134311 Cov.: 33 AF XY: 0.424 AC XY: 307277AN XY: 725204
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GnomAD4 genome ? AF: 0.503 AC: 76316AN: 151860Hom.: 20360 Cov.: 31 AF XY: 0.500 AC XY: 37116AN XY: 74200
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 05, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at