rs10837774

Positions:

• chr11-5302158-G-A
• chr11-5302158-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000292896.3(HBE1):​c.-266-32002C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 152,022 control chromosomes in the GnomAD database, including 4,256 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 0.23 (4256 hom., cov: 32)
• Consequence: HBE1 ENST00000292896.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.855

Genes affected

HBE1 (HGNC:4830): (hemoglobin subunit epsilon 1) The epsilon globin gene (HBE) is normally expressed in the embryonic yolk sac: two epsilon chains together with two zeta chains (an alpha-like globin) constitute the embryonic hemoglobin Hb Gower I; two epsilon chains together with two alpha chains form the embryonic Hb Gower II. Both of these embryonic hemoglobins are normally supplanted by fetal, and later, adult hemoglobin. The five beta-like globin genes are found within a 45 kb cluster on chromosome 11 in the following order: 5'-epsilon - G-gamma - A-gamma - delta - beta-3' [provided by RefSeq, Jul 2008]

HBG2 (HGNC:4832): (hemoglobin subunit gamma 2) The gamma globin genes (HBG1 and HBG2) are normally expressed in the fetal liver, spleen and bone marrow. Two gamma chains together with two alpha chains constitute fetal hemoglobin (HbF) which is normally replaced by adult hemoglobin (HbA) at birth. In some beta-thalassemias and related conditions, gamma chain production continues into adulthood. The two types of gamma chains differ at residue 136 where glycine is found in the G-gamma product (HBG2) and alanine is found in the A-gamma product (HBG1). The former is predominant at birth. The order of the genes in the beta-globin cluster is: 5'- epsilon -- gamma-G -- gamma-A -- delta -- beta--3'. [provided by RefSeq, Jul 2008]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.273 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
HBE1	ENST00000292896.3	c.-266-32002C>T		intron_variant		1		ENSP00000292896	P1
HBE1	ENST00000380237.5	c.-309-20207C>T		intron_variant		1		ENSP00000369586	P1
HBG2	ENST00000380252.6	c.-73-47644C>T		intron_variant		3		ENSP00000369602
	ENST00000646569.1	n.58+26198C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34187 AN: 151904 Hom.: 4253 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.225 AC: 34211 AN: 152022 Hom.: 4256 Cov.: 32 AF XY: 0.221 AC XY: 16409 AN XY: 74306

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.233

Gnomad4 EAS AF: 0.143

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.236

Alfa AF: 0.188 Hom.: 638

Bravo AF: 0.230

Asia WGS AF: 0.214 AC: 744 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.61
DANN	Benign	0.33

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10837774; hg19: chr11-5323388;