chr11-5253363-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_000184.3(HBG2):c.358G>A(p.Gly120Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000459 in 1,613,494 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G120R) has been classified as Uncertain significance.
Frequency
Consequence
NM_000184.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HBG2 | NM_000184.3 | c.358G>A | p.Gly120Ser | missense_variant | 3/3 | ENST00000336906.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HBG2 | ENST00000336906.6 | c.358G>A | p.Gly120Ser | missense_variant | 3/3 | 1 | NM_000184.3 | P1 | |
HBG2 | ENST00000380252.6 | c.193G>A | p.Gly65Ser | missense_variant | 3/3 | 3 | |||
HBG2 | ENST00000444587.1 | downstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 151950Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251044Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135670
GnomAD4 exome AF: 0.0000486 AC: 71AN: 1461544Hom.: 0 Cov.: 32 AF XY: 0.0000399 AC XY: 29AN XY: 727112
GnomAD4 genome AF: 0.0000197 AC: 3AN: 151950Hom.: 0 Cov.: 32 AF XY: 0.0000270 AC XY: 2AN XY: 74192
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 17, 2022 | The c.358G>A (p.G120S) alteration is located in exon 3 (coding exon 3) of the HBG2 gene. This alteration results from a G to A substitution at nucleotide position 358, causing the glycine (G) at amino acid position 120 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at