chr1-45006112-T-C
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_024602.6(HECTD3):āc.1730A>Gā(p.Asn577Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00115 in 1,613,788 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.0042 ( 5 hom., cov: 31)
Exomes š: 0.00083 ( 2 hom. )
Consequence
HECTD3
NM_024602.6 missense
NM_024602.6 missense
Scores
4
12
Clinical Significance
Conservation
PhyloP100: 3.48
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 Likely_benign. Variant got -6 ACMG points.
BP6
Variant 1-45006112-T-C is Benign according to our data. Variant chr1-45006112-T-C is described in ClinVar as [Benign]. Clinvar id is 711828.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 5 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HECTD3 | NM_024602.6 | c.1730A>G | p.Asn577Ser | missense_variant | 14/21 | ENST00000372172.5 | |
HECTD3 | XM_047430487.1 | c.878A>G | p.Asn293Ser | missense_variant | 12/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HECTD3 | ENST00000372172.5 | c.1730A>G | p.Asn577Ser | missense_variant | 14/21 | 5 | NM_024602.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00424 AC: 646AN: 152196Hom.: 5 Cov.: 31
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GnomAD3 exomes AF: 0.00117 AC: 290AN: 248784Hom.: 2 AF XY: 0.000919 AC XY: 124AN XY: 134988
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GnomAD4 exome AF: 0.000827 AC: 1208AN: 1461474Hom.: 2 Cov.: 31 AF XY: 0.000784 AC XY: 570AN XY: 726984
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GnomAD4 genome AF: 0.00424 AC: 646AN: 152314Hom.: 5 Cov.: 31 AF XY: 0.00442 AC XY: 329AN XY: 74476
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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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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Uncertain
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
B;B
Vest4
MVP
MPC
0.36
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AG_spliceai
Position offset: -1
Find out detailed SpliceAI scores and Pangolin per-transcript scores at