11-5234352-C-A
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BS2_Supporting
The NM_000519.4(HBD):c.82G>T(p.Ala28Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00187 in 1,613,812 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000519.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00164 AC: 249AN: 152200Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00216 AC: 542AN: 251342Hom.: 6 AF XY: 0.00241 AC XY: 328AN XY: 135846
GnomAD4 exome AF: 0.00190 AC: 2775AN: 1461494Hom.: 16 Cov.: 30 AF XY: 0.00209 AC XY: 1523AN XY: 727104
GnomAD4 genome AF: 0.00163 AC: 249AN: 152318Hom.: 1 Cov.: 32 AF XY: 0.00172 AC XY: 128AN XY: 74490
ClinVar
Submissions by phenotype
not provided Pathogenic:3
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Commonly referred to as the Hb A2-Yialousa variant and has been reported numerous times in the literature and is the most common variant identified in the HBD gene in individuals from the Mediterranean area (PMID: 26754299, 23797957, 23215833, 1742490, 3401592); Published functional studies demonstrate that this variant may affect RNA splicing by strengthening an upstream cryptic splice donor site (PMID: 8900178); In silico analysis supports that this missense variant has a deleterious effect on splicing; In silico analysis indicates that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 12402333, 3401592, 1742490, 9054695, 23215833, 1398286, 25333069, 27884173, 20854114, 26754299, 27461962, 23797957, 30487145, 31980526, 34426522, 31688628, 31589614, 33178177, 10975439, 35930292, 37605839, 8900178) -
delta Thalassemia Pathogenic:2
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NM_000519.3:c.82G>T in the HBD gene has an allele frequency of 0.008 in Ashkenazi Jewish subpopulation in the gnomAD database. The HBD c.82G>T (p.Ala28Ser) was the most common variant found in the HBD gene in a Iran cohort with thalassemia (PMID: 26754299). In addition, De Angioletti et al. also reported that the Hb A2-Yialousa (g.82G>T) was the most prevalent (42/63 families). Functional studies indicate that A28S may affect RNA splicing by strengthening an upstream cryptic splice donor site (PMID: 1742490). Taken together, we interprete this variant as Pathogenic/Likely pathogenic. ACMG/AMP Criteria applied: PS4; PP4; PS3. -
Glucocorticoid-remediable aldosteronism Pathogenic:1
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Fetal hemoglobin quantitative trait locus 1 Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
HEMOGLOBIN A(2) YIALOUSA Other:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at