1-45003724-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_024602.6(HECTD3):c.2446G>A(p.Ala816Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000155 in 1,613,978 control chromosomes in the GnomAD database, including 1 homozygotes. 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 Likely benign (★).
Frequency
Consequence
NM_024602.6 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HECTD3 | NM_024602.6 | c.2446G>A | p.Ala816Thr | missense_variant | 20/21 | ENST00000372172.5 | |
HECTD3 | XM_047430487.1 | c.1594G>A | p.Ala532Thr | missense_variant | 18/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HECTD3 | ENST00000372172.5 | c.2446G>A | p.Ala816Thr | missense_variant | 20/21 | 5 | NM_024602.6 | P1 | |
HECTD3 | ENST00000486132.5 | n.1293G>A | non_coding_transcript_exon_variant | 5/6 | 1 | ||||
HECTD3 | ENST00000372168.7 | c.1276G>A | p.Ala426Thr | missense_variant | 12/13 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 151998Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000309 AC: 77AN: 249548Hom.: 2 AF XY: 0.000295 AC XY: 40AN XY: 135394
GnomAD4 exome AF: 0.000159 AC: 232AN: 1461862Hom.: 1 Cov.: 33 AF XY: 0.000166 AC XY: 121AN XY: 727242
GnomAD4 genome AF: 0.000118 AC: 18AN: 152116Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74354
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 02, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at