rs7619173

chr3-181279171-C-T

Variant summary

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

The NR_075091.1(SOX2-OT):n.218+103588C>T 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 0.48 in 151,982 control chromosomes in the GnomAD database, including 21,001 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 0.48 (21001 hom., cov: 33)
• Consequence: SOX2-OT NR_075091.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.120

Genes affected

SOX2-OT (HGNC:20209): (SOX2 overlapping transcript) This gene produces alternatively spliced long non-coding RNAs. These RNAs were observed to be upregulated in tumor cells and positively correlated to expression of the SRY-box 2 gene. Overexpression of these transcripts may promote cell proliferation. [provided by RefSeq, Dec 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.81 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SOX2-OT	NR_075091.1	n.218+103588C>T		intron_variant, non_coding_transcript_variant
SOX2-OT	NR_075092.1	n.218+103588C>T		intron_variant, non_coding_transcript_variant
SOX2-OT	NR_075093.1	n.194+103588C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SOX2-OT	ENST00000626948.3	n.272+103588C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72870 AN: 151864 Hom.: 20939 Cov.: 33

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.480 AC: 72993 AN: 151982 Hom.: 21001 Cov.: 33 AF XY: 0.470 AC XY: 34905 AN XY: 74312

Gnomad4 AFR AF: 0.817

Gnomad4 AMR AF: 0.359

Gnomad4 ASJ AF: 0.431

Gnomad4 EAS AF: 0.262

Gnomad4 SAS AF: 0.432

Gnomad4 FIN AF: 0.273

Gnomad4 NFE AF: 0.358

Gnomad4 OTH AF: 0.481

Alfa AF: 0.380 Hom.: 12090

Bravo AF: 0.498

Asia WGS AF: 0.440 AC: 1527 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	4.6
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: rs7619173; hg19: chr3-180996959;