chr3-181404262-C-A

Position:

• chr3-181404262-C-A

Variant summary

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

The NR_075091.1(SOX2-OT):​n.219-159458C>A 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 0.413 in 151,958 control chromosomes in the GnomAD database, including 15,167 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 0.41 (15167 hom., cov: 32)
• Consequence: SOX2-OT NR_075091.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.53 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SOX2-OT	NR_075091.1	n.219-159458C>A		intron_variant, non_coding_transcript_variant
SOX2-OT	NR_075092.1	n.219-159458C>A		intron_variant, non_coding_transcript_variant
SOX2-OT	NR_075093.1	n.195-159458C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SOX2-OT	ENST00000626948.3	n.273-159458C>A		intron_variant, non_coding_transcript_variant		5
	ENST00000663941.1	n.528+17072G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62672 AN: 151840 Hom.: 15161 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.413 AC: 62699 AN: 151958 Hom.: 15167 Cov.: 32 AF XY: 0.415 AC XY: 30853 AN XY: 74262

Gnomad4 AFR AF: 0.164

Gnomad4 AMR AF: 0.422

Gnomad4 ASJ AF: 0.476

Gnomad4 EAS AF: 0.347

Gnomad4 SAS AF: 0.386

Gnomad4 FIN AF: 0.626

Gnomad4 NFE AF: 0.535

Gnomad4 OTH AF: 0.412

Alfa AF: 0.478 Hom.: 5997

Bravo AF: 0.383

Asia WGS AF: 0.362 AC: 1263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs733422; hg19: chr3-181122050;