rs35317336

Positions:

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 6P and 8B. PM2PP3_StrongBP6_Very_Strong

The NM_000558.5(HBA1):​c.163C>G​(p.Gln55Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q55R) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 31)

Consequence

HBA1
NM_000558.5 missense

Scores

6
2
10

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:2O:5

Conservation

PhyloP100: -0.244
Variant links:
Genes affected
HBA1 (HGNC:4823): (hemoglobin subunit alpha 1) The human alpha globin gene cluster located on chromosome 16 spans about 30 kb and includes seven loci: 5'- zeta - pseudozeta - mu - pseudoalpha-1 - alpha-2 - alpha-1 - theta - 3'. The alpha-2 (HBA2) and alpha-1 (HBA1) coding sequences are identical. These genes differ slightly over the 5' untranslated regions and the introns, but they differ significantly over the 3' untranslated regions. Two alpha chains plus two beta chains constitute HbA, which in normal adult life comprises about 97% of the total hemoglobin; alpha chains combine with delta chains to constitute HbA-2, which with HbF (fetal hemoglobin) makes up the remaining 3% of adult hemoglobin. Alpha thalassemias result from deletions of each of the alpha genes as well as deletions of both HBA2 and HBA1; some nondeletion alpha thalassemias have also been reported. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.955
BP6
Variant 16-176996-C-G is Benign according to our data. Variant chr16-176996-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 15782.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
HBA1NM_000558.5 linkuse as main transcriptc.163C>G p.Gln55Glu missense_variant 2/3 ENST00000320868.9 NP_000549.1 P69905D1MGQ2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
HBA1ENST00000320868.9 linkuse as main transcriptc.163C>G p.Gln55Glu missense_variant 2/31 NM_000558.5 ENSP00000322421.5 P69905
HBA1ENST00000472694.1 linkuse as main transcriptn.299C>G non_coding_transcript_exon_variant 1/21
HBA1ENST00000487791.1 linkuse as main transcriptn.132C>G non_coding_transcript_exon_variant 2/21
HBA1ENST00000397797.1 linkuse as main transcriptc.67C>G p.Gln23Glu missense_variant 2/32 ENSP00000380899.1 G3V1N2

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
Cov.:
16
GnomAD4 genome
Cov.:
31

ClinVar

Significance: Benign/Likely benign
Submissions summary: Benign:2Other:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Likely benign, criteria provided, single submitterclinical testingQuest Diagnostics Nichols Institute San Juan CapistranoDec 29, 2020- -
Benign, criteria provided, single submitterclinical testingARUP Laboratories, Molecular Genetics and Genomics, ARUP LaboratoriesDec 15, 2021- -
HEMOGLOBIN J (MEXICO) Other:1
other, no assertion criteria providedliterature onlyOMIMJul 20, 2016- -
HEMOGLOBIN MEXICO Other:1
other, no assertion criteria providedliterature onlyOMIMJul 20, 2016- -
HEMOGLOBIN J (PARIS 2) Other:1
other, no assertion criteria providedliterature onlyOMIMJul 20, 2016- -
HEMOGLOBIN UPPSALA Other:1
other, no assertion criteria providedliterature onlyOMIMJul 20, 2016- -
HEMOGLOBIN J Other:1
other, no assertion criteria providedliterature onlyOMIMJul 20, 2016- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.13
BayesDel_addAF
Pathogenic
0.32
D
BayesDel_noAF
Pathogenic
0.22
CADD
Benign
17
DANN
Benign
0.97
DEOGEN2
Benign
0.21
T;.
Eigen
Benign
-0.44
Eigen_PC
Benign
-0.59
FATHMM_MKL
Benign
0.16
N
LIST_S2
Uncertain
0.94
D;D
M_CAP
Pathogenic
0.57
D
MetaRNN
Pathogenic
0.95
D;D
MetaSVM
Uncertain
0.044
D
PrimateAI
Benign
0.42
T
PROVEAN
Benign
-2.3
N;N
REVEL
Pathogenic
0.66
Sift
Pathogenic
0.0
D;D
Sift4G
Benign
0.14
T;T
Vest4
0.59
MutPred
0.87
Loss of methylation at K57 (P = 0.0824);.;
MVP
0.99
ClinPred
0.51
D
GERP RS
2.2
Varity_R
0.80
gMVP
0.82

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

Publications

LitVar

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

Other links and lift over

dbSNP: rs35317336; hg19: chr16-226995; API