12-93589778-C-T

Position:

• chr12-93589778-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XM_011538935.2(SOCS2):​c.591+14605C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 152,106 control chromosomes in the GnomAD database, including 8,312 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 0.32 (8312 hom., cov: 33)
• Consequence: SOCS2 XM_011538935.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.587

Genes affected

SOCS2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SOCS2	XM_011538935.2	c.591+14605C>T		intron_variant			XP_011537237.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48449 AN: 151986 Hom.: 8290 Cov.: 33

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.319 AC: 48521 AN: 152106 Hom.: 8312 Cov.: 33 AF XY: 0.315 AC XY: 23400 AN XY: 74356

Gnomad4 AFR AF: 0.459

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.338

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.265

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.291

Alfa AF: 0.266 Hom.: 11256

Bravo AF: 0.330

Asia WGS AF: 0.268 AC: 936 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	15
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7953508; hg19: chr12-93983554;