rs778119481
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_000521.4(HEXB):c.160C>A(p.Pro54Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000212 in 1,600,640 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P54S) has been classified as Uncertain significance.
Frequency
Consequence
NM_000521.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HEXB | NM_000521.4 | c.160C>A | p.Pro54Thr | missense_variant | 1/14 | ENST00000261416.12 | |
HEXB | NM_001292004.2 | c.-376-3908C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HEXB | ENST00000261416.12 | c.160C>A | p.Pro54Thr | missense_variant | 1/14 | 1 | NM_000521.4 | P1 | |
HEXB | ENST00000511181.5 | c.-376-3908C>A | intron_variant | 1 | |||||
HEXB | ENST00000513079.5 | n.225C>A | non_coding_transcript_exon_variant | 1/6 | 2 | ||||
HEXB | ENST00000515528.1 | n.215C>A | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000659 AC: 1AN: 151684Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000144 AC: 31AN: 214966Hom.: 0 AF XY: 0.000101 AC XY: 12AN XY: 119300
GnomAD4 exome AF: 0.0000228 AC: 33AN: 1448956Hom.: 0 Cov.: 31 AF XY: 0.0000180 AC XY: 13AN XY: 720248
GnomAD4 genome ? AF: 0.00000659 AC: 1AN: 151684Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74088
ClinVar
Submissions by phenotype
Sandhoff disease Pathogenic:1Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 24, 2023 | - - |
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Oct 28, 2019 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Daryl Scott Lab, Baylor College of Medicine | Nov 10, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at