6-135031510-G-C

Variant names:

• chr6-135031510-G-C
• rs9321481
• NM_006620.4:c.430+8063C>G

Variant summary

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

The NM_006620.4(HBS1L):​c.430+8063C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 151,790 control chromosomes in the GnomAD database, including 18,447 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 0.49 (18447 hom., cov: 32)
• Consequence: HBS1L NM_006620.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0960
• Publications: 7 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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006620.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HBS1L	NM_006620.4	MANE Select	c.430+8063C>G		intron	N/A	NP_006611.1	Q9Y450-1
	HBS1L	NM_001145158.2		c.304+8063C>G		intron	N/A	NP_001138630.1	Q9Y450-4
	HBS1L	NM_001363686.2		c.-209+8063C>G		intron	N/A	NP_001350615.1	B7Z524

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HBS1L	ENST00000367837.10	TSL:1 MANE Select	c.430+8063C>G		intron	N/A	ENSP00000356811.5	Q9Y450-1
	HBS1L	ENST00000949311.1		c.430+8063C>G		intron	N/A	ENSP00000619370.1
	HBS1L	ENST00000881131.1		c.430+8063C>G		intron	N/A	ENSP00000551190.1

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74208 AN: 151674 Hom.: 18422 Cov.: 32

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.489 AC: 74275 AN: 151790 Hom.: 18447 Cov.: 32 AF XY: 0.495 AC XY: 36671 AN XY: 74104

African (AFR) AF: 0.440 AC: 18225 AN: 41450

American (AMR) AF: 0.489 AC: 7477 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.483 AC: 1673 AN: 3466

East Asian (EAS) AF: 0.533 AC: 2754 AN: 5170

South Asian (SAS) AF: 0.565 AC: 2723 AN: 4820

European-Finnish (FIN) AF: 0.611 AC: 6335 AN: 10360

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.495 AC: 33644 AN: 67930

Other (OTH) AF: 0.474 AC: 997 AN: 2104

Alfa AF: 0.494 Hom.: 2268

Bravo AF: 0.476

Asia WGS AF: 0.568 AC: 1975 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.4
DANN	Benign	0.57
PhyloP100		0.096
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs9321481; hg19: chr6-135352648;