12-112167334-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.12517G>A(p.Val4173Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000962 in 1,612,018 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/15 in silico tools predict 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
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HECTD4 | NM_001388303.1 | c.12517G>A | p.Val4173Ile | missense_variant | 72/76 | ENST00000682272.1 | NP_001375232.1 | |
HECTD4 | NM_001109662.4 | c.12547G>A | p.Val4183Ile | missense_variant | 72/76 | NP_001103132.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HECTD4 | ENST00000682272.1 | c.12517G>A | p.Val4173Ile | missense_variant | 72/76 | NM_001388303.1 | ENSP00000507687 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152238Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000646 AC: 16AN: 247856Hom.: 0 AF XY: 0.0000818 AC XY: 11AN XY: 134454
GnomAD4 exome AF: 0.0000966 AC: 141AN: 1459780Hom.: 0 Cov.: 31 AF XY: 0.0000937 AC XY: 68AN XY: 726004
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152238Hom.: 0 Cov.: 33 AF XY: 0.0000941 AC XY: 7AN XY: 74388
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 15, 2023 | The c.12001G>A (p.V4001I) 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 12001, causing the valine (V) at amino acid position 4001 to be replaced by an isoleucine (I). 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