rs10492321

chr12-93586312-T-Achr12-93586312-T-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

SOCS2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SOCS2	XM_011538935.2	c.591+11139T>A		intron_variant
SOCS2	XM_011538929.2			downstream_gene_variant
SOCS2	XM_011538936.2			downstream_gene_variant
SOCS2	XR_944810.2			downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.323

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.233

Gnomad4 NFE AF: 0.222

Gnomad4 OTH AF: 0.184

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	8.3
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10492321; hg19: chr12-93980088;