1-45007592-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_024602.6(HECTD3):c.1324G>A(p.Val442Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000386 in 1,608,282 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024602.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HECTD3 | NM_024602.6 | c.1324G>A | p.Val442Met | missense_variant | 10/21 | ENST00000372172.5 | |
HECTD3 | XM_047430487.1 | c.472G>A | p.Val158Met | missense_variant | 8/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HECTD3 | ENST00000372172.5 | c.1324G>A | p.Val442Met | missense_variant | 10/21 | 5 | NM_024602.6 | P1 | |
HECTD3 | ENST00000372168.7 | c.154G>A | p.Val52Met | missense_variant | 2/13 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000246 AC: 6AN: 243958Hom.: 0 AF XY: 0.0000301 AC XY: 4AN XY: 132790
GnomAD4 exome AF: 0.0000419 AC: 61AN: 1456128Hom.: 0 Cov.: 34 AF XY: 0.0000386 AC XY: 28AN XY: 724560
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152154Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 11, 2022 | The c.1324G>A (p.V442M) alteration is located in exon 10 (coding exon 10) of the HECTD3 gene. This alteration results from a G to A substitution at nucleotide position 1324, causing the valine (V) at amino acid position 442 to be replaced by a methionine (M). 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