rs113665733
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_006620.4(HBS1L):c.130C>T(p.Arg44Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000443 in 1,612,452 control chromosomes in the GnomAD database, including 5 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: 32)
Exomes 𝑓: 0.00024 ( 4 hom. )
Consequence
HBS1L
NM_006620.4 missense
NM_006620.4 missense
Scores
5
7
6
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.05
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 -8 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.010869116).
BS2
?
High Homozygotes in GnomAdExome4 at 4 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HBS1L | NM_006620.4 | c.130C>T | p.Arg44Trp | missense_variant | 3/18 | ENST00000367837.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HBS1L | ENST00000367837.10 | c.130C>T | p.Arg44Trp | missense_variant | 3/18 | 1 | NM_006620.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00240 AC: 365AN: 152136Hom.: 1 Cov.: 32
GnomAD3 genomes
?
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GnomAD3 exomes AF: 0.000639 AC: 160AN: 250386Hom.: 3 AF XY: 0.000517 AC XY: 70AN XY: 135324
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GnomAD4 exome AF: 0.000240 AC: 351AN: 1460198Hom.: 4 Cov.: 30 AF XY: 0.000245 AC XY: 178AN XY: 726402
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GnomAD4 genome ? AF: 0.00239 AC: 364AN: 152254Hom.: 1 Cov.: 32 AF XY: 0.00240 AC XY: 179AN XY: 74438
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T;T;T;T;.;.;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Pathogenic
D;D;D;D;D;D;D
MetaRNN
Benign
T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Pathogenic
M;.;.;.;.;M;.
MutationTaster
Benign
D;D;D;D;D;D;D;N
PrimateAI
Benign
T
PROVEAN
Uncertain
D;D;D;D;D;D;D
REVEL
Pathogenic
Sift
Pathogenic
D;D;D;D;D;D;D
Sift4G
Uncertain
D;D;D;.;.;D;D
Polyphen
D;.;.;.;.;D;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
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