16-28866221-C-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001387430.1(SH2B1):c.127C>A(p.Arg43Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000106 in 1,609,210 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. R43C) has been classified as Uncertain significance.
Frequency
Consequence
NM_001387430.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SH2B1 | NM_001387430.1 | c.127C>A | p.Arg43Ser | missense_variant | 1/8 | ENST00000684370.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SH2B1 | ENST00000684370.1 | c.127C>A | p.Arg43Ser | missense_variant | 1/8 | NM_001387430.1 | P3 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152038Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000846 AC: 2AN: 236518Hom.: 0 AF XY: 0.00000769 AC XY: 1AN XY: 130064
GnomAD4 exome AF: 0.0000110 AC: 16AN: 1457172Hom.: 0 Cov.: 35 AF XY: 0.00000690 AC XY: 5AN XY: 724796
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152038Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74234
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Sep 06, 2023 | This sequence change replaces arginine, which is basic and polar, with serine, which is neutral and polar, at codon 43 of the SH2B1 protein (p.Arg43Ser). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This missense change has been observed in individual(s) with SH2B1-related conditions (PMID: 26031769). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at