rs1376742145
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_000521.4(HEXB):c.512-3C>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000288 in 1,390,626 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000521.4 splice_region, intron
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HEXB | NM_000521.4 | c.512-3C>A | splice_region_variant, intron_variant | Intron 3 of 13 | ENST00000261416.12 | NP_000512.2 | ||
HEXB | NM_001292004.2 | c.-164-3C>A | splice_region_variant, intron_variant | Intron 3 of 13 | NP_001278933.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HEXB | ENST00000261416.12 | c.512-3C>A | splice_region_variant, intron_variant | Intron 3 of 13 | 1 | NM_000521.4 | ENSP00000261416.7 | |||
HEXB | ENST00000511181.5 | c.-164-3C>A | splice_region_variant, intron_variant | Intron 3 of 13 | 1 | ENSP00000426285.1 | ||||
HEXB | ENST00000510820.1 | n.231-3C>A | splice_region_variant, intron_variant | Intron 1 of 3 | 3 | |||||
HEXB | ENST00000513079.5 | n.577-3C>A | splice_region_variant, intron_variant | Intron 3 of 5 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152156Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000242 AC: 3AN: 1238470Hom.: 0 Cov.: 20 AF XY: 0.00000159 AC XY: 1AN XY: 627184
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152156Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74322
ClinVar
Submissions by phenotype
Sandhoff disease Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at