rs10492321

Variant names:

• chr12-93586312-T-A
• rs10492321
• XM_011538935.2:c.591+11139T>A

Your query was ambiguous. Multiple possible variants found:

• chr12-93586312-T-A
• chr12-93586312-T-C
• chr12-93586312-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_011538935.2(SOCS2):​c.591+11139T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 152,238 control chromosomes in the GnomAD database, including 3,215 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 0.20 (3215 hom., cov: 33)
• Consequence: SOCS2 XM_011538935.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0200
• Publications: 14 publications found

Genes affected

SOCS2 (HGNC:19382): (suppressor of cytokine signaling 2) This gene encodes a member of the suppressor of cytokine signaling (SOCS) family. SOCS family members are cytokine-inducible negative regulators of cytokine receptor signaling via the Janus kinase/signal transducer and activation of transcription pathway (the JAK/STAT pathway). SOCS family proteins interact with major molecules of signaling complexes to block further signal transduction, in part, by proteasomal depletion of receptors or signal-transducing proteins via ubiquitination. The expression of this gene can be induced by a subset of cytokines, including erythropoietin, GM-CSF, IL10, interferon (IFN)-gamma and by cytokine receptors such as growth horomone receptor. The protein encoded by this gene interacts with the cytoplasmic domain of insulin-like growth factor-1 receptor (IGF1R) and is thought to be involved in the regulation of IGF1R mediated cell signaling. This gene has pseudogenes on chromosomes 20 and 22. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2012]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30568 AN: 152120 Hom.: 3211 Cov.: 33

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.187

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.201 AC: 30593 AN: 152238 Hom.: 3215 Cov.: 33 AF XY: 0.200 AC XY: 14911 AN XY: 74438

African (AFR) AF: 0.148 AC: 6131 AN: 41558

American (AMR) AF: 0.232 AC: 3544 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 429 AN: 3468

East Asian (EAS) AF: 0.323 AC: 1673 AN: 5184

South Asian (SAS) AF: 0.139 AC: 671 AN: 4830

European-Finnish (FIN) AF: 0.233 AC: 2469 AN: 10578

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.222 AC: 15107 AN: 68002

Other (OTH) AF: 0.184 AC: 389 AN: 2114

Alfa AF: 0.220 Hom.: 482

Bravo AF: 0.201

Asia WGS AF: 0.192 AC: 669 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.3
DANN	Benign	0.78
PhyloP100		0.020

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10492321; hg19: chr12-93980088;