chr4-88649863-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM2PP2BP4_Moderate
The NM_014606.3(HERC3):c.250C>G(p.Gln84Glu) variant causes a missense change. The variant allele was found at a frequency of 0.00000753 in 1,461,696 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000075 ( 0 hom. )
Consequence
HERC3
NM_014606.3 missense
NM_014606.3 missense
Scores
2
16
Clinical Significance
Conservation
PhyloP100: 3.80
Genes affected
HERC3 (HGNC:4876): (HECT and RLD domain containing E3 ubiquitin protein ligase 3) This gene encodes a member the HERC ubiquitin ligase family. The encoded protein is located in the cytosol and binds ubiquitin via a HECT domain. Mutations in this gene have been associated with colorectal and gastric carcinomas. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Oct 2012]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PP2
?
Missense variant where missense usually causes diseases, HERC3
BP4
?
Computational evidence support a benign effect (MetaRNN=0.1569398).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HERC3 | NM_014606.3 | c.250C>G | p.Gln84Glu | missense_variant | 4/26 | ENST00000402738.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HERC3 | ENST00000402738.6 | c.250C>G | p.Gln84Glu | missense_variant | 4/26 | 1 | NM_014606.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251048Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135664
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GnomAD4 exome AF: 0.00000753 AC: 11AN: 1461696Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7AN XY: 727124
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GnomAD4 genome ? Cov.: 32
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Cov.:
32
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1
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 26, 2023 | The c.250C>G (p.Q84E) alteration is located in exon 4 (coding exon 2) of the HERC3 gene. This alteration results from a C to G substitution at nucleotide position 250, causing the glutamine (Q) at amino acid position 84 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T;T;.;.;.;T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
M_CAP
Benign
D
MetaRNN
Benign
T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;.;.;N;.;.;N
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N;N;N;N;N
REVEL
Benign
Sift
Benign
T;T;T;T;T;T;T
Sift4G
Benign
T;T;T;T;T;T;T
Polyphen
B;.;.;.;.;.;B
Vest4
MutPred
Gain of disorder (P = 0.184);Gain of disorder (P = 0.184);Gain of disorder (P = 0.184);Gain of disorder (P = 0.184);Gain of disorder (P = 0.184);Gain of disorder (P = 0.184);Gain of disorder (P = 0.184);
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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Calibrated prediction
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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