rs10859525

Variant names:

• chr12-93554681-G-A
• rs10859525
• ENST00000499137.6:n.430-9323C>T

Variant summary

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

The ENST00000499137.6(SOCS2-AS1):​n.430-9323C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 151,784 control chromosomes in the GnomAD database, including 14,279 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 0.43 (14279 hom., cov: 30)
• Consequence: SOCS2-AS1 ENST00000499137.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.571
• Publications: 9 publications found

Genes affected

SOCS2-AS1 (HGNC:27054): (SOCS2 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000499137.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SOCS2-AS1	ENST00000499137.6	TSL:1	n.430-9323C>T		intron	N/A
	SOCS2-AS1	ENST00000500986.6	TSL:2	n.526-9323C>T		intron	N/A
	SOCS2-AS1	ENST00000547845.5	TSL:5	n.476-3169C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65131 AN: 151666 Hom.: 14280 Cov.: 30

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.628

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.429 AC: 65147 AN: 151784 Hom.: 14279 Cov.: 30 AF XY: 0.429 AC XY: 31794 AN XY: 74144

African (AFR) AF: 0.475 AC: 19665 AN: 41364

American (AMR) AF: 0.449 AC: 6851 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1227 AN: 3468

East Asian (EAS) AF: 0.628 AC: 3228 AN: 5140

South Asian (SAS) AF: 0.445 AC: 2138 AN: 4808

European-Finnish (FIN) AF: 0.378 AC: 3972 AN: 10516

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.392 AC: 26604 AN: 67920

Other (OTH) AF: 0.460 AC: 967 AN: 2104

Alfa AF: 0.416 Hom.: 19282

Bravo AF: 0.441

Asia WGS AF: 0.507 AC: 1760 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.1
DANN	Benign	0.71
PhyloP100		0.57

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10859525;

hg19: chr12-93948457;