chr3-181593779-C-T

Position:

• chr3-181593779-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.428-17082C>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 0.299 in 151,962 control chromosomes in the GnomAD database, including 7,128 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 0.30 (7128 hom., cov: 32)
• Consequence: SOX2-OT NR_075091.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.732

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SOX2-OT	NR_075091.1	n.428-17082C>T		intron_variant, non_coding_transcript_variant
SOX2-OT	NR_075092.1	n.428-17082C>T		intron_variant, non_coding_transcript_variant
SOX2-OT	NR_075093.1	n.404-17082C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SOX2-OT	ENST00000626948.3	n.482-17082C>T		intron_variant, non_coding_transcript_variant		5
	ENST00000636224.2	n.718-10942G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45431 AN: 151844 Hom.: 7134 Cov.: 32

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.299 AC: 45433 AN: 151962 Hom.: 7128 Cov.: 32 AF XY: 0.295 AC XY: 21869 AN XY: 74256

Gnomad4 AFR AF: 0.374

Gnomad4 AMR AF: 0.301

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.185

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.278

Gnomad4 OTH AF: 0.297

Alfa AF: 0.276 Hom.: 3082

Bravo AF: 0.308

Asia WGS AF: 0.168 AC: 585 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.8
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9839776; hg19: chr3-181311567;