10-91460472-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_182765.6(HECTD2):c.314G>A(p.Arg105His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000105 in 1,611,610 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. R105C) 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 -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HECTD2 | NM_182765.6 | c.314G>A | p.Arg105His | missense_variant | 3/21 | ENST00000298068.10 | |
HECTD2-AS1 | NR_024467.1 | n.426+64556C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HECTD2 | ENST00000298068.10 | c.314G>A | p.Arg105His | missense_variant | 3/21 | 1 | NM_182765.6 | P4 | |
ENST00000688440.1 | n.321+64556C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000855 AC: 13AN: 152034Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000681 AC: 17AN: 249642Hom.: 0 AF XY: 0.0000815 AC XY: 11AN XY: 134962
GnomAD4 exome AF: 0.000107 AC: 156AN: 1459458Hom.: 0 Cov.: 29 AF XY: 0.000101 AC XY: 73AN XY: 726024
GnomAD4 genome ? AF: 0.0000854 AC: 13AN: 152152Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74372
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 14, 2021 | The c.314G>A (p.R105H) alteration is located in exon 3 (coding exon 3) of the HECTD2 gene. This alteration results from a G to A substitution at nucleotide position 314, causing the arginine (R) at amino acid position 105 to be replaced by a histidine (H). 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