rs4788102
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001308293.2(SH2B1):c.-171+330G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 151,972 control chromosomes in the GnomAD database, including 9,507 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.34 ( 9506 hom., cov: 32)
Exomes 𝑓: 0.38 ( 1 hom. )
Consequence
SH2B1
NM_001308293.2 intron
NM_001308293.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0810
Genes affected
SH2B1 (HGNC:30417): (SH2B adaptor protein 1) This gene encodes a member of the SH2-domain containing mediators family. The encoded protein mediates activation of various kinases and may function in cytokine and growth factor receptor signaling and cellular transformation. Alternatively spliced transcript variants have been described. [provided by RefSeq, Mar 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SH2B1 | NM_001308293.2 | c.-171+330G>A | intron_variant | NP_001295222.1 | ||||
SH2B1 | NM_001387404.1 | c.-170-1591G>A | intron_variant | NP_001374333.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SH2B1 | ENST00000322610.12 | c.-171+330G>A | intron_variant | 2 | ENSP00000321221 | P3 | ||||
SH2B1 | ENST00000563591.5 | c.-170-1591G>A | intron_variant | 2 | ENSP00000458097 | |||||
SH2B1 | ENST00000567536.5 | c.-116+330G>A | intron_variant | 3 | ENSP00000455236 |
Frequencies
GnomAD3 genomes AF: 0.341 AC: 51700AN: 151830Hom.: 9477 Cov.: 32
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GnomAD4 exome AF: 0.375 AC: 9AN: 24Hom.: 1 AF XY: 0.444 AC XY: 8AN XY: 18
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GnomAD4 genome AF: 0.341 AC: 51793AN: 151948Hom.: 9506 Cov.: 32 AF XY: 0.339 AC XY: 25188AN XY: 74250
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ClinVar
Not reported inComputational scores
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Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at