rs35959442
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000529882.5(HBS1L):c.-26G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 324,586 control chromosomes in the GnomAD database, including 12,377 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 0.29 ( 6867 hom., cov: 31)
Exomes 𝑓: 0.23 ( 5510 hom. )
Consequence
HBS1L
ENST00000529882.5 5_prime_UTR
ENST00000529882.5 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0970
Genes affected
HBS1L (HGNC:4834): (HBS1 like translational GTPase) This gene encodes a member of the GTP-binding elongation factor family. It is expressed in multiple tissues with the highest expression in heart and skeletal muscle. The intergenic region of this gene and the MYB gene has been identified to be a quantitative trait locus (QTL) controlling fetal hemoglobin level, and this region influnces erythrocyte, platelet, and monocyte counts as well as erythrocyte volume and hemoglobin content. DNA polymorphisms at this region associate with fetal hemoglobin levels and pain crises in sickle cell disease. A single nucleotide polymorphism in exon 1 of this gene is significantly associated with severity in beta-thalassemia/Hemoglobin E. Multiple alternatively spliced transcript variants encoding different protein isoforms have been found for this gene. [provided by RefSeq, May 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
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Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HBS1L | ENST00000529882.5 | c.-26G>C | 5_prime_UTR_variant | 1/5 | 4 | ENSP00000433030 |
Frequencies
GnomAD3 genomes AF: 0.291 AC: 44218AN: 151758Hom.: 6847 Cov.: 31
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GnomAD3 exomes AF: 0.235 AC: 6037AN: 25652Hom.: 828 AF XY: 0.227 AC XY: 3468AN XY: 15278
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GnomAD4 exome AF: 0.233 AC: 40314AN: 172712Hom.: 5510 Cov.: 0 AF XY: 0.219 AC XY: 22427AN XY: 102310
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GnomAD4 genome AF: 0.292 AC: 44273AN: 151874Hom.: 6867 Cov.: 31 AF XY: 0.289 AC XY: 21424AN XY: 74228
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ClinVar
Not reported inComputational scores
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at