12-112167391-C-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBS1_Supporting
The NM_001388303.1(HECTD4):c.12460G>A(p.Glu4154Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000787 in 1,613,690 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001388303.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HECTD4 | ENST00000682272.1 | c.12460G>A | p.Glu4154Lys | missense_variant | Exon 72 of 76 | NM_001388303.1 | ENSP00000507687.1 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152222Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000401 AC: 10AN: 249088Hom.: 0 AF XY: 0.0000518 AC XY: 7AN XY: 135128
GnomAD4 exome AF: 0.0000807 AC: 118AN: 1461468Hom.: 0 Cov.: 31 AF XY: 0.0000770 AC XY: 56AN XY: 727032
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152222Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74368
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.11944G>A (p.E3982K) alteration is located in exon 71 (coding exon 70) of the HECTD4 gene. This alteration results from a G to A substitution at nucleotide position 11944, causing the glutamic acid (E) at amino acid position 3982 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at