rs34623271

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 1P and 0B. PM4_Supporting

The NM_000517.6(HBA2):​c.19_21del​(p.Asp7del) variant causes a inframe deletion change involving the alteration of a conserved nucleotide. Variant has been reported in ClinVar as other (no stars). Synonymous variant affecting the same amino acid position (i.e. A6A) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 0)

Consequence

HBA2
NM_000517.6 inframe_deletion

Scores

Not classified

Clinical Significance

other no assertion criteria provided O:1

Conservation

PhyloP100: 8.93
Variant links:
Genes affected
HBA2 (HGNC:4824): (hemoglobin subunit alpha 2) 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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM4
Nonframeshift variant in NON repetitive region in NM_000517.6. Strenght limited to Supporting due to length of the change: 1aa.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
HBA2NM_000517.6 linkuse as main transcriptc.19_21del p.Asp7del inframe_deletion 1/3 ENST00000251595.11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
HBA2ENST00000251595.11 linkuse as main transcriptc.19_21del p.Asp7del inframe_deletion 1/31 NM_000517.6 P1
HBA2ENST00000482565.1 linkuse as main transcriptn.38_40del non_coding_transcript_exon_variant 1/21
HBA2ENST00000397806.1 linkuse as main transcriptc.-29_-27del 5_prime_UTR_variant 1/32
HBA2ENST00000484216.1 linkuse as main transcript upstream_gene_variant 1

Frequencies

GnomAD3 genomes
Cov.:
0
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
0

ClinVar

Significance: other
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

HEMOGLOBIN BOYLE HEIGHTS Other:1
other, no assertion criteria providedliterature onlyOMIMSep 12, 2022- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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: rs34623271; hg19: chr16-222928; API