rs3750396
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_016848.6(SHC3):c.*6185C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.588 in 152,160 control chromosomes in the GnomAD database, including 27,859 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 0.59 ( 27847 hom., cov: 32)
Exomes 𝑓: 0.49 ( 12 hom. )
Consequence
SHC3
NM_016848.6 3_prime_UTR
NM_016848.6 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.527
Genes affected
SHC3 (HGNC:18181): (SHC adaptor protein 3) Enables phosphotyrosine residue binding activity. Predicted to be involved in transmembrane receptor protein tyrosine kinase signaling pathway. Predicted to act upstream of or within glutamatergic synaptic transmission and learning or memory. Predicted to be located in cytosol. 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=-0.87).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.784 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SHC3 | NM_016848.6 | c.*6185C>T | 3_prime_UTR_variant | 12/12 | ENST00000375835.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SHC3 | ENST00000375835.9 | c.*6185C>T | 3_prime_UTR_variant | 12/12 | 1 | NM_016848.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.588 AC: 89326AN: 151944Hom.: 27806 Cov.: 32
GnomAD3 genomes
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GnomAD4 exome AF: 0.490 AC: 48AN: 98Hom.: 12 Cov.: 0 AF XY: 0.462 AC XY: 36AN XY: 78
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GnomAD4 genome ? AF: 0.588 AC: 89422AN: 152062Hom.: 27847 Cov.: 32 AF XY: 0.581 AC XY: 43170AN XY: 74300
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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