rs1464502

Positions:

• chr12-24235155-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_120472.1(SOX5-AS1):​n.446-2667A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 152,120 control chromosomes in the GnomAD database, including 8,059 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 (8059 hom., cov: 33)
• Consequence: SOX5-AS1 NR_120472.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800

Genes affected

SOX5-AS1 (HGNC:53311): (SOX5 antisense RNA 1)

SOX5 (HGNC:11201): (SRY-box transcription factor 5) This gene encodes a member of the SOX (SRY-related HMG-box) family of transcription factors involved in the regulation of embryonic development and in the determination of the cell fate. The encoded protein may act as a transcriptional regulator after forming a protein complex with other proteins. The encoded protein may play a role in chondrogenesis. A pseudogene of this gene is located on chromosome 8. Multiple transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SOX5-AS1	NR_120472.1	n.446-2667A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SOX5-AS1	ENST00000668875.1	n.280-2667A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.317 AC: 48120 AN: 152002 Hom.: 8035 Cov.: 33

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.0782

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.317 AC: 48186 AN: 152120 Hom.: 8059 Cov.: 33 AF XY: 0.312 AC XY: 23203 AN XY: 74352

Gnomad4 AFR AF: 0.384

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.0786

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.273

Gnomad4 NFE AF: 0.324

Gnomad4 OTH AF: 0.307

Alfa AF: 0.321 Hom.: 4492

Bravo AF: 0.316

Asia WGS AF: 0.159 AC: 554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1464502; hg19: chr12-24388089;