17-78360015-T-G
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000330871.3(SOCS3):c.-354A>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.9 in 201,872 control chromosomes in the GnomAD database, including 82,065 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 0.91 ( 62760 hom., cov: 35)
Exomes 𝑓: 0.87 ( 19305 hom. )
Consequence
SOCS3
ENST00000330871.3 5_prime_UTR
ENST00000330871.3 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.75
Genes affected
SOCS3 (HGNC:19391): (suppressor of cytokine signaling 3) This gene encodes a member of the STAT-induced STAT inhibitor (SSI), also known as suppressor of cytokine signaling (SOCS), family. SSI family members are cytokine-inducible negative regulators of cytokine signaling. The expression of this gene is induced by various cytokines, including IL6, IL10, and interferon (IFN)-gamma. The protein encoded by this gene can bind to JAK2 kinase, and inhibit the activity of JAK2 kinase. Studies of the mouse counterpart of this gene suggested the roles of this gene in the negative regulation of fetal liver hematopoiesis, and placental development. [provided by RefSeq, Jul 2008]
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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=-0.85).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.928 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SOCS3 | NM_003955.5 | c.-354A>C | 5_prime_UTR_variant | 1/2 | ENST00000330871.3 | NP_003946.3 | ||
SOCS3 | NM_001378933.1 | c.-88-832A>C | intron_variant | NP_001365862.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SOCS3 | ENST00000330871.3 | c.-354A>C | 5_prime_UTR_variant | 1/2 | 1 | NM_003955.5 | ENSP00000330341 | P1 | ||
SOCS3 | ENST00000587578.1 | c.-255A>C | 5_prime_UTR_variant | 1/2 | 4 | ENSP00000464727 |
Frequencies
GnomAD3 genomes AF: 0.908 AC: 137693AN: 151622Hom.: 62707 Cov.: 35
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GnomAD4 exome AF: 0.875 AC: 43851AN: 50142Hom.: 19305 Cov.: 0 AF XY: 0.876 AC XY: 23133AN XY: 26410
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GnomAD4 genome AF: 0.908 AC: 137801AN: 151730Hom.: 62760 Cov.: 35 AF XY: 0.907 AC XY: 67263AN XY: 74156
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ClinVar
Not reported inComputational scores
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Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at