rs35959442

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0970
Variant links:
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

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
HBS1LENST00000529882.5 linkuse as main transcriptc.-26G>C 5_prime_UTR_variant 1/54 ENSP00000433030

Frequencies

GnomAD3 genomes
AF:
0.291
AC:
44218
AN:
151758
Hom.:
6847
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.365
Gnomad AMI
AF:
0.190
Gnomad AMR
AF:
0.236
Gnomad ASJ
AF:
0.239
Gnomad EAS
AF:
0.279
Gnomad SAS
AF:
0.112
Gnomad FIN
AF:
0.347
Gnomad MID
AF:
0.239
Gnomad NFE
AF:
0.270
Gnomad OTH
AF:
0.255
GnomAD3 exomes
AF:
0.235
AC:
6037
AN:
25652
Hom.:
828
AF XY:
0.227
AC XY:
3468
AN XY:
15278
show subpopulations
Gnomad AFR exome
AF:
0.366
Gnomad AMR exome
AF:
0.223
Gnomad ASJ exome
AF:
0.232
Gnomad EAS exome
AF:
0.304
Gnomad SAS exome
AF:
0.124
Gnomad FIN exome
AF:
0.359
Gnomad NFE exome
AF:
0.271
Gnomad OTH exome
AF:
0.249
GnomAD4 exome
AF:
0.233
AC:
40314
AN:
172712
Hom.:
5510
Cov.:
0
AF XY:
0.219
AC XY:
22427
AN XY:
102310
show subpopulations
Gnomad4 AFR exome
AF:
0.329
Gnomad4 AMR exome
AF:
0.206
Gnomad4 ASJ exome
AF:
0.223
Gnomad4 EAS exome
AF:
0.290
Gnomad4 SAS exome
AF:
0.116
Gnomad4 FIN exome
AF:
0.347
Gnomad4 NFE exome
AF:
0.267
Gnomad4 OTH exome
AF:
0.262
GnomAD4 genome
AF:
0.292
AC:
44273
AN:
151874
Hom.:
6867
Cov.:
31
AF XY:
0.289
AC XY:
21424
AN XY:
74228
show subpopulations
Gnomad4 AFR
AF:
0.365
Gnomad4 AMR
AF:
0.236
Gnomad4 ASJ
AF:
0.239
Gnomad4 EAS
AF:
0.280
Gnomad4 SAS
AF:
0.112
Gnomad4 FIN
AF:
0.347
Gnomad4 NFE
AF:
0.270
Gnomad4 OTH
AF:
0.257
Alfa
AF:
0.157
Hom.:
311
Bravo
AF:
0.292
Asia WGS
AF:
0.206
AC:
716
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
8.3
DANN
Benign
0.62

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs35959442; hg19: chr6-135424179; API