chr6-135097778-A-G

Variant names:

• chr6-135097778-A-G
• rs7776054
• ENST00000529882.5:c.88+5150T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000529882.5(HBS1L):​c.88+5150T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 152,084 control chromosomes in the GnomAD database, including 4,617 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 0.24 (4617 hom., cov: 32)
• Consequence: HBS1L ENST00000529882.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.763
• Publications: 65 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HBS1L	ENST00000529882.5	c.88+5150T>C		intron_variant	Intron 1 of 4	4		ENSP00000433030.1

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36398 AN: 151966 Hom.: 4612 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.200

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.239 AC: 36420 AN: 152084 Hom.: 4617 Cov.: 32 AF XY: 0.238 AC XY: 17697 AN XY: 74358

African (AFR) AF: 0.217 AC: 8995 AN: 41456

American (AMR) AF: 0.180 AC: 2757 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 806 AN: 3464

East Asian (EAS) AF: 0.256 AC: 1329 AN: 5188

South Asian (SAS) AF: 0.111 AC: 534 AN: 4828

European-Finnish (FIN) AF: 0.346 AC: 3653 AN: 10544

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.261 AC: 17716 AN: 67992

Other (OTH) AF: 0.200 AC: 423 AN: 2114

Alfa AF: 0.254 Hom.: 15747

Bravo AF: 0.230

Asia WGS AF: 0.180 AC: 624 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	6.9
DANN	Benign	0.82
PhyloP100		0.76

Splicing

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

Other links and lift over

dbSNP: rs7776054; hg19: chr6-135418916;