rs7633815

chr3-181738126-A-Cchr3-181738126-A-G

Variant summary

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

The NR_075091.1(SOX2-OT):n.891-1443A>C 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 0.661 in 152,032 control chromosomes in the GnomAD database, including 33,612 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 0.66 (33612 hom., cov: 31)
• Consequence: SOX2-OT NR_075091.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.752 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SOX2-OT	NR_075091.1	n.891-1443A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SOX2-OT	ENST00000626948.3	n.944+22834A>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.661 AC: 100347 AN: 151914 Hom.: 33564 Cov.: 31

Gnomad AFR AF: 0.758

Gnomad AMI AF: 0.633

Gnomad AMR AF: 0.735

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.643

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.656

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

GnomAD4 genome AF: 0.661 AC: 100443 AN: 152032 Hom.: 33612 Cov.: 31 AF XY: 0.658 AC XY: 48908 AN XY: 74306

Gnomad4 AFR AF: 0.759

Gnomad4 AMR AF: 0.735

Gnomad4 ASJ AF: 0.605

Gnomad4 EAS AF: 0.643

Gnomad4 SAS AF: 0.535

Gnomad4 FIN AF: 0.601

Gnomad4 NFE AF: 0.607

Gnomad4 OTH AF: 0.655

Alfa AF: 0.624 Hom.: 24023

Bravo AF: 0.680

Asia WGS AF: 0.576 AC: 2002 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.69
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7633815; hg19: chr3-181455914;