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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SOCS2-AS1	ENST00000499137.6	n.430-9323C>T		intron_variant	Intron 2 of 2	1
SOCS2-AS1	ENST00000500986.6	n.526-9323C>T		intron_variant	Intron 3 of 4	2
SOCS2-AS1	ENST00000547845.5	n.476-3169C>T		intron_variant	Intron 3 of 3	5

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 v4.3

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

Other links and lift over

dbSNP: rs10859525; hg19: chr12-93948457;