rs9806753
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_203349.4(SHC4):c.841-2078T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.659 in 151,988 control chromosomes in the GnomAD database, including 33,931 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 0.66 ( 33931 hom., cov: 32)
Consequence
SHC4
NM_203349.4 intron
NM_203349.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.442
Genes affected
SHC4 (HGNC:16743): (SHC adaptor protein 4) Predicted to enable receptor tyrosine kinase binding activity. Predicted to be involved in transmembrane receptor protein tyrosine kinase signaling pathway. Predicted to act upstream of or within several processes, including apoptotic process; positive regulation of cell population proliferation; and stem cell differentiation. Predicted to be located in postsynaptic membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.97).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.737 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SHC4 | NM_203349.4 | c.841-2078T>C | intron_variant | ENST00000332408.9 | |||
SHC4 | XM_005254375.4 | c.292-2078T>C | intron_variant | ||||
SHC4 | XM_047432492.1 | c.-18-2078T>C | intron_variant | ||||
SHC4 | XM_047432493.1 | c.-18-2078T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SHC4 | ENST00000332408.9 | c.841-2078T>C | intron_variant | 1 | NM_203349.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.659 AC: 100069AN: 151870Hom.: 33925 Cov.: 32
GnomAD3 genomes
?
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100069
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.659 AC: 100120AN: 151988Hom.: 33931 Cov.: 32 AF XY: 0.653 AC XY: 48506AN XY: 74262
GnomAD4 genome
?
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100120
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32
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48506
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74262
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2296
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at