12-112163651-C-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 3P and 4B. PM2PP2BP4_Strong
The NM_001388303.1(HECTD4):c.12788G>A(p.Arg4263Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000177 in 1,540,968 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00038 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00015 ( 0 hom. )
Consequence
HECTD4
NM_001388303.1 missense
NM_001388303.1 missense
Scores
5
4
5
Clinical Significance
Conservation
PhyloP100: 7.39
Genes affected
HECTD4 (HGNC:26611): (HECT domain E3 ubiquitin protein ligase 4) Predicted to enable ubiquitin-protein transferase activity. Involved in glucose homeostasis and glucose metabolic process. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -1 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PP2
?
Missense variant where missense usually causes diseases, HECTD4
BP4
?
Computational evidence support a benign effect (MetaRNN=0.024242133).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HECTD4 | NM_001388303.1 | c.12788G>A | p.Arg4263Gln | missense_variant | 74/76 | ENST00000682272.1 | |
HECTD4 | NM_001109662.4 | c.12818G>A | p.Arg4273Gln | missense_variant | 74/76 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HECTD4 | ENST00000682272.1 | c.12788G>A | p.Arg4263Gln | missense_variant | 74/76 | NM_001388303.1 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000381 AC: 58AN: 152222Hom.: 1 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.000308 AC: 44AN: 142882Hom.: 0 AF XY: 0.000275 AC XY: 21AN XY: 76424
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GnomAD4 exome AF: 0.000155 AC: 215AN: 1388628Hom.: 0 Cov.: 33 AF XY: 0.000152 AC XY: 104AN XY: 684690
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GnomAD4 genome ? AF: 0.000381 AC: 58AN: 152340Hom.: 1 Cov.: 32 AF XY: 0.000456 AC XY: 34AN XY: 74500
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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 | Dec 05, 2022 | The c.12272G>A (p.R4091Q) alteration is located in exon 73 (coding exon 72) of the HECTD4 gene. This alteration results from a G to A substitution at nucleotide position 12272, causing the arginine (R) at amino acid position 4091 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Pathogenic
Cadd
Pathogenic
Dann
Pathogenic
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D;D
PrimateAI
Uncertain
T
REVEL
Uncertain
Sift4G
Benign
T;T
Vest4
MVP
MPC
ClinPred
T
GERP RS
gMVP
Splicing
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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