rs4789777
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001330542.2(HEXD):c.632-13G>A variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00181 in 1,603,112 control chromosomes in the GnomAD database, including 20 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0024 ( 1 hom., cov: 34)
Exomes 𝑓: 0.0018 ( 19 hom. )
Consequence
HEXD
NM_001330542.2 splice_polypyrimidine_tract, intron
NM_001330542.2 splice_polypyrimidine_tract, intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.674
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BS2
?
High Homozygotes in GnomAdExome4 at 19 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HEXD | NM_001330542.2 | c.632-13G>A | splice_polypyrimidine_tract_variant, intron_variant | ENST00000327949.15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HEXD | ENST00000327949.15 | c.632-13G>A | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001330542.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00236 AC: 359AN: 152138Hom.: 1 Cov.: 34
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GnomAD3 exomes AF: 0.00215 AC: 496AN: 230950Hom.: 2 AF XY: 0.00214 AC XY: 269AN XY: 125916
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GnomAD4 exome AF: 0.00175 AC: 2542AN: 1450856Hom.: 19 Cov.: 32 AF XY: 0.00187 AC XY: 1349AN XY: 721256
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GnomAD4 genome ? AF: 0.00236 AC: 359AN: 152256Hom.: 1 Cov.: 34 AF XY: 0.00232 AC XY: 173AN XY: 74436
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at