10-91460471-C-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4
The NM_182765.6(HECTD2):c.313C>T(p.Arg105Cys) variant causes a missense change. The variant allele was found at a frequency of 0.00000685 in 1,459,070 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R105H) has been classified as Uncertain significance.
Frequency
Consequence
NM_182765.6 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 | UniProt |
---|---|---|---|---|---|---|---|
HECTD2 | NM_182765.6 | c.313C>T | p.Arg105Cys | missense_variant | 3/21 | ENST00000298068.10 | |
HECTD2-AS1 | NR_024467.1 | n.426+64557G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HECTD2 | ENST00000298068.10 | c.313C>T | p.Arg105Cys | missense_variant | 3/21 | 1 | NM_182765.6 | P4 | |
ENST00000688440.1 | n.321+64557G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000802 AC: 2AN: 249462Hom.: 0 AF XY: 0.00000741 AC XY: 1AN XY: 134886
GnomAD4 exome AF: 0.00000685 AC: 10AN: 1459070Hom.: 0 Cov.: 30 AF XY: 0.00000689 AC XY: 5AN XY: 725864
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 17, 2023 | The c.313C>T (p.R105C) alteration is located in exon 3 (coding exon 3) of the HECTD2 gene. This alteration results from a C to T substitution at nucleotide position 313, causing the arginine (R) at amino acid position 105 to be replaced by a cysteine (C). 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