16-11255329-GGGGGCC-GGGGGCCGGGGCC
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_003745.2(SOCS1):c.144_149dupGGCCCC(p.Pro50_Gly51insAlaPro) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000389 in 1,464,428 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000046 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000038 ( 0 hom. )
Consequence
SOCS1
NM_003745.2 disruptive_inframe_insertion
NM_003745.2 disruptive_inframe_insertion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.39
Genes affected
SOCS1 (HGNC:19383): (suppressor of cytokine signaling 1) 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 can be induced by a subset of cytokines, including IL2, IL3 erythropoietin (EPO), CSF2/GM-CSF, and interferon (IFN)-gamma. The protein encoded by this gene functions downstream of cytokine receptors, and takes part in a negative feedback loop to attenuate cytokine signaling. Knockout studies in mice suggested the role of this gene as a modulator of IFN-gamma action, which is required for normal postnatal growth and survival. [provided by RefSeq, Jul 2008]
RMI2 (HGNC:28349): (RecQ mediated genome instability 2) RMI2 is a component of the BLM (RECQL3; MIM 604610) complex, which plays a role in homologous recombination-dependent DNA repair and is essential for genome stability (Xu et al., 2008 [PubMed 18923082]).[supplied by OMIM, Nov 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BS2
High AC in GnomAd4 at 7 AD gene.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000461 AC: 7AN: 151950Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000855 AC: 6AN: 70188Hom.: 0 AF XY: 0.000122 AC XY: 5AN XY: 40826
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GnomAD4 exome AF: 0.0000381 AC: 50AN: 1312478Hom.: 0 Cov.: 32 AF XY: 0.0000387 AC XY: 25AN XY: 646376
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GnomAD4 genome AF: 0.0000461 AC: 7AN: 151950Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74234
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at