chr5-74685274-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_000521.4(HEXB):c.14G>A(p.Gly5Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000937 in 1,388,096 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars). Synonymous variant affecting the same amino acid position (i.e. G5G) has been classified as Likely benign.
Frequency
Consequence
NM_000521.4 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 |
---|---|---|---|---|---|---|---|
HEXB | NM_000521.4 | c.14G>A | p.Gly5Glu | missense_variant | 1/14 | ENST00000261416.12 | |
HEXB | NM_001292004.2 | c.-376-4054G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HEXB | ENST00000261416.12 | c.14G>A | p.Gly5Glu | missense_variant | 1/14 | 1 | NM_000521.4 | P1 | |
HEXB | ENST00000511181.5 | c.-376-4054G>A | intron_variant | 1 | |||||
HEXB | ENST00000513079.5 | n.79G>A | non_coding_transcript_exon_variant | 1/6 | 2 | ||||
HEXB | ENST00000515528.1 | n.69G>A | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD3 exomes AF: 0.00000719 AC: 1AN: 139060Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 76522
GnomAD4 exome AF: 0.00000937 AC: 13AN: 1388096Hom.: 0 Cov.: 30 AF XY: 0.0000131 AC XY: 9AN XY: 685594
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
Sandhoff disease Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Aug 15, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at