1-45006731-G-A
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_024602.6(HECTD3):c.1686C>T(p.Thr562=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000768 in 1,613,686 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0039 ( 3 hom., cov: 32)
Exomes 𝑓: 0.00044 ( 2 hom. )
Consequence
HECTD3
NM_024602.6 synonymous
NM_024602.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.232
Genes affected
HECTD3 (HGNC:26117): (HECT domain E3 ubiquitin protein ligase 3) The protein encoded by this gene transfers ubiquitin from an E2 ubiquitin-conjugating enzyme to targeted substrates, leading to the degradation of those substrates. The encoded protein has been shown to transfer ubiquitin to TRIOBP to facilitate cell cycle progression, and to STX8. [provided by RefSeq, Dec 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.49).
BP6
Variant 1-45006731-G-A is Benign according to our data. Variant chr1-45006731-G-A is described in ClinVar as [Benign]. Clinvar id is 711829.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.232 with no splicing effect.
BS2
High Homozygotes in GnomAd4 at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HECTD3 | NM_024602.6 | c.1686C>T | p.Thr562= | synonymous_variant | 13/21 | ENST00000372172.5 | |
HECTD3 | XM_047430487.1 | c.834C>T | p.Thr278= | synonymous_variant | 11/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HECTD3 | ENST00000372172.5 | c.1686C>T | p.Thr562= | synonymous_variant | 13/21 | 5 | NM_024602.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00388 AC: 591AN: 152124Hom.: 3 Cov.: 32
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GnomAD3 exomes AF: 0.000956 AC: 238AN: 249064Hom.: 0 AF XY: 0.000748 AC XY: 101AN XY: 135076
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GnomAD4 exome AF: 0.000439 AC: 641AN: 1461444Hom.: 2 Cov.: 31 AF XY: 0.000376 AC XY: 273AN XY: 726968
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GnomAD4 genome AF: 0.00393 AC: 598AN: 152242Hom.: 3 Cov.: 32 AF XY: 0.00364 AC XY: 271AN XY: 74434
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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 | Invitae | Jul 15, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
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Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at