rs334

Variant names:

• chr11-5227002-T-A
• rs334
• NM_000518.5:c.20A>T

Your query was ambiguous. Multiple possible variants found:

• chr11-5227002-T-A
• chr11-5227002-T-G
• chr11-5227002-T-C

Variant summary

Our verdict is Likely pathogenic. The variant received 7 ACMG points: 16P and 9B. PS3 PM1 PM5 PP5_Very_Strong BP4 BA1

The NM_000518.5(HBB):​c.20A>T​(p.Glu7Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00265 in 1,610,650 control chromosomes in the GnomAD database, including 40 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). ClinVar reports functional evidence for this variant: "SCV000914520: In mice expressing the sickle trait variant, erythrocytes were shown to sickle with deoxygenation, similar to that seen in humans with sickle cell anemia (PMID:2296310), and in mice with 100% expression of the sickle cell variant, chronic hemolytic anemia with circulating sickled erythrocytes, as well as chronic tissue damage, was observed (PMID:12124399)." and additional evidence is available in ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E7K) has been classified as Likely pathogenic.

• Frequency:
  • Genomes: 𝑓 0.013 (9 hom., cov: 32)
  • Exomes 𝑓: 0.0016 (31 hom.)
• Consequence: HBB NM_000518.5 missense
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:63 B:1 O:4
• Conservation: PhyloP100: 0.690
• Publications: 547 publications found

Genes affected

HBB (HGNC:4827): (hemoglobin subunit beta) The alpha (HBA) and beta (HBB) loci determine the structure of the 2 types of polypeptide chains in adult hemoglobin, Hb A. The normal adult hemoglobin tetramer consists of two alpha chains and two beta chains. Mutant beta globin causes sickle cell anemia. Absence of beta chain causes beta-zero-thalassemia. Reduced amounts of detectable beta globin causes beta-plus-thalassemia. 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]

HBB Gene-Disease associations (from GenCC):

• dominant beta-thalassemia

  Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), ClinGen, Orphanet
• erythrocytosis, familial, 6

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), Genomics England PanelApp, ClinGen
• hemoglobin M disease

  Inheritance: AD Classification: DEFINITIVE, MODERATE, SUPPORTIVE Submitted by: Ambry Genetics, ClinGen, Orphanet
• unstable hemoglobin disease

  Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
• beta thalassemia

  Inheritance: AR Classification: DEFINITIVE Submitted by: Myriad Women’s Health
• beta-thalassemia HBB/LCRB

  Inheritance: AR, SD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, ClinGen
• sickle cell disease and related diseases

  Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
• Heinz body anemia

  Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• sickle cell disease

  Inheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet
• hereditary persistence of fetal hemoglobin-beta-thalassemia syndrome

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• beta-thalassemia intermedia

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• beta-thalassemia major

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• delta-beta-thalassemia

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• hemoglobin C disease

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• hemoglobin C-beta-thalassemia syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• hemoglobin E disease

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• hemoglobin E-beta-thalassemia syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• hereditary persistence of fetal hemoglobin-sickle cell disease syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• sickle cell-beta-thalassemia disease syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• sickle cell-hemoglobin c disease syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• sickle cell-hemoglobin d disease syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• sickle cell-hemoglobin E disease syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ENSG00000298932 (HGNC:):

ACMG classification

Our verdict: Likely_pathogenic. The variant received 7 ACMG points.

• PS3: PS3 evidence extracted from ClinVar submissions: SCV000914520: In mice expressing the sickle trait variant, erythrocytes were shown to sickle with deoxygenation, similar to that seen in humans with sickle cell anemia (PMID: 2296310), and in mice with 100% expression of the sickle cell variant, chronic hemolytic anemia with circulating sickled erythrocytes, as well as chronic tissue damage, was observed (PMID: 12124399).; SCV000967671: In vitro functional studies support an impact on protein function as this variant is shown to affect hemoglobin polymerization, resulting in abnormally shaped red blood cells (He 2017 PMID: 12124399, Adachi 1991 PMID: 1802884). Transgenic mouse models have also shown that this variant causes sickle cell disease, as mouse red blood cells with the variant had a sickle shape upon deoxygenation (Greaves 1990 PMID: 2296310).; SCV001423600: "This alteration is supported by well-established in vitro or in vivo functional studies to have a damaging effect on protein function or splicing [PS3]."; SCV002058326: Functional studies provide strong evidence of the variant having a damaging effect on the gene or gene product (PMID: 12124399, 1802884, 2296310, 28356267).; SCV003845197: Experimental studies have shown that this missense change affects HBB function by Eshbach ML, et, al, 2017.; SCV004048527: Experimental studies have shown that this missense change affects HBB function (Eshbach ML et al., 2017).; SCV000321760: Functional studies using transgenic mouse models showed mouse erythrocytes with this variant sickled upon deoxygenation (Greaves et al., 1990) and kinetic studies indicate this variant drastically decreases the molecular stability of the protein (Adachi et al., 1987);; SCV000949988: Experimental studies have shown that this missense change affects HBB function (PMID: 1802884, 12124399, 28356267).; SCV001142414: Experimental studies have shown that this missense change affects hemoglobin polymerization and can result in abnormally-shaped red blood cells (PMID: 12124399; 28356267; 1802884).; SCV002767565: Additionally, functional studies showed that erythrocytes from transgenic mice expressing human HBB sickle readily on deoxygenation (Greaves, D.R. et al., 1990).; SCV000741189: "The p.E7V alteration is known to significantly decrease the solubility of the hemoglobin protein, allowing for the polymerization that ultimately results in red cell sickling (Adachi, 1987)."; SCV001360653: The most pronounced variant effect results in decreased solubility of deoxygenated Hb S, and polymerization which leads to the formation of an extensive network of fibers in red blood cells (example, Adachi_1991).; SCV002107097: "Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product (PMID: 13464827; 11880644; 11830454; 12124399; 28356267; 1802884) - PS3."; SCV005060996: Experimental studies have shown that this mutation (Glu7Val) in hemoglobin (Hb) causes red blood cells to assume a rigid curved shape that blocks their passage through the vasculature resulting in ischemia, severe pain, and necrosis (Eshbach et al. 2017).; SCV003839051: Experimental studies have shown that this variant affects the physical and kinetic properties of the hemoglobin protein.
• PM1: In a hotspot region, there are 3 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 11 benign, 30 uncertain in NM_000518.5
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr11-5227003-C-T is described in ClinVar as Pathogenic/Likely_pathogenic. ClinVar VariationId is 15126.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• PP5: Variant 11-5227002-T-A is Pathogenic according to our data. Variant chr11-5227002-T-A is described in ClinVar as Pathogenic. ClinVar VariationId is 15333.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP4: Computational evidence support a benign effect (MetaRNN=0.007841617). . Strength limited to SUPPORTING due to the PP5.
• BA1: GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0547 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000518.5. 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
	HBB	NM_000518.5	MANE Select	c.20A>T	p.Glu7Val	missense	Exon 1 of 3	NP_000509.1	D9YZU5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HBB	ENST00000335295.4	TSL:1 MANE Select	c.20A>T	p.Glu7Val	missense	Exon 1 of 3	ENSP00000333994.3	P68871
	HBB	ENST00000485743.1	TSL:1	c.20A>T	p.Glu7Val	missense	Exon 1 of 2	ENSP00000496200.1	A0A2R8Y7R2
	HBB	ENST00000647020.1		c.20A>T	p.Glu7Val	missense	Exon 1 of 3	ENSP00000494175.1	P68871

Frequencies

GnomAD3 genomes AF: 0.0127 AC: 1926 AN: 152176 Hom.: 9 Cov.: 32

Gnomad AFR AF: 0.0434

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00589

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00228

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000162

Gnomad OTH AF: 0.00718

GnomAD2 exomes AF: 0.00348 AC: 874 AN: 251180 AF XY: 0.00266

Gnomad AFR exome AF: 0.0470

Gnomad AMR exome AF: 0.00217

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000528

Gnomad OTH exome AF: 0.00163

GnomAD4 exome AF: 0.00160 AC: 2335 AN: 1458356 Hom.: 31 Cov.: 33 AF XY: 0.00145 AC XY: 1054 AN XY: 725764

African (AFR) AF: 0.0569 AC: 1897 AN: 33354

American (AMR) AF: 0.00244 AC: 109 AN: 44718

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26114

East Asian (EAS) AF: 0.00 AC: 0 AN: 39668

South Asian (SAS) AF: 0.000812 AC: 70 AN: 86214

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53408

Middle Eastern (MID) AF: 0.00399 AC: 23 AN: 5758

European-Non Finnish (NFE) AF: 0.0000316 AC: 35 AN: 1108842

Other (OTH) AF: 0.00333 AC: 201 AN: 60280

GnomAD4 genome AF: 0.0127 AC: 1937 AN: 152294 Hom.: 9 Cov.: 32 AF XY: 0.0122 AC XY: 912 AN XY: 74478

African (AFR) AF: 0.0436 AC: 1810 AN: 41554

American (AMR) AF: 0.00588 AC: 90 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5186

South Asian (SAS) AF: 0.00228 AC: 11 AN: 4826

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10610

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000162 AC: 11 AN: 68030

Other (OTH) AF: 0.00710 AC: 15 AN: 2112

Alfa AF: 0.000514 Hom.: 0

ESP6500AA AF: 0.0402 AC: 177

ESP6500EA AF: 0.000233 AC: 2

ExAC AF: 0.00439 AC: 533

Asia WGS AF: 0.0130 AC: 47 AN: 3476

EpiCase AF: 0.000218

EpiControl AF: 0.000178

ClinVar

ClinVar submissions

Significance: Pathogenic

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
21	-	-	Hb SS disease (22)
18	-	-	not provided (18)
5	-	-	beta Thalassemia (6)
4	-	-	Beta-thalassemia HBB/LCRB (4)
4	-	-	HBB-related disorder (5)
1	-	-	alpha Thalassemia;C0002895:Hb SS disease;C0005283:beta Thalassemia;C0700299:Heinz body anemia;C1840779:METHEMOGLOBINEMIA, BETA TYPE;C1841621:Fetal hemoglobin quantitative trait locus 1;C1858990:Dominant beta-thalassemia;C1970028:Malaria, susceptibility to;C4693822:Erythrocytosis, familial, 6 (1)
1	-	-	alpha Thalassemia;C0002895:Hb SS disease;C0700299:Heinz body anemia;C1858990:Dominant beta-thalassemia;CN322236:Beta-thalassemia HBB/LCRB (1)
1	-	-	Fetal hemoglobin quantitative trait locus 1 (1)
1	-	-	Hb SS disease;C0005283:beta Thalassemia;C0700299:Heinz body anemia;C1841621:Fetal hemoglobin quantitative trait locus 1;C1858990:Dominant beta-thalassemia;C1970028:Malaria, susceptibility to (1)
1	-	-	Hb SS disease;C0019025:Hereditary persistence of fetal hemoglobin;C0700299:Heinz body anemia;C1840779:METHEMOGLOBINEMIA, BETA TYPE;C1858990:Dominant beta-thalassemia;C1970028:Malaria, susceptibility to;C4693822:Erythrocytosis, familial, 6;CN322236:Beta-thalassemia HBB/LCRB (1)
1	-	-	Hereditary persistence of fetal hemoglobin (1)
1	-	-	Inborn genetic diseases (1)
1	-	-	Malaria, susceptibility to (1)
1	-	-	See cases (1)
1	-	-	Sickle cell disease and related diseases (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.22
BayesDel_addAF	Benign	-0.18	T
BayesDel_noAF	Uncertain	0.0
CADD	Benign	14
DANN	Benign	0.96
DEOGEN2	Benign	0.11	T
Eigen	Benign	-0.74
Eigen_PC	Benign	-0.85
FATHMM_MKL	Benign	0.40	N
LIST_S2	Benign	0.60	T
MetaRNN	Benign	0.0078	T
MetaSVM	Benign	-0.60	T
MutationAssessor	Pathogenic	3.6	H
PhyloP100		0.69
PrimateAI	Benign	0.38	T
PROVEAN	Pathogenic	-4.8	D
REVEL	Uncertain	0.54
Sift	Uncertain	0.025	D
Sift4G	Benign	0.063	T
Polyphen		0.0010	B
Vest4		0.54
MVP		0.95
MPC		0.037
ClinPred		0.049	T
GERP RS		0.15
PromoterAI		-0.047	Neutral
Varity_R		0.51
gMVP		0.63
Mutation Taster		=3/97	disease causing (ClinVar)

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: rs334; hg19: chr11-5248232;