chr3-181264288-A-C

Variant names:

• chr3-181264288-A-C
• rs2718771
• ENST00000460739.6:n.213+88705A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000460739.6(SOX2-OT):​n.213+88705A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.867 in 151,896 control chromosomes in the GnomAD database, including 57,237 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 0.87 (57237 hom., cov: 30)
• Consequence: SOX2-OT ENST00000460739.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000460739.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SOX2-OT	NR_075091.1		n.218+88705A>C		intron	N/A
	SOX2-OT	NR_075092.1		n.218+88705A>C		intron	N/A
	SOX2-OT	NR_075093.1		n.194+88705A>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SOX2-OT	ENST00000460739.6	TSL:4	n.213+88705A>C		intron	N/A
	SOX2-OT	ENST00000469278.5	TSL:4	n.194+88705A>C		intron	N/A
	SOX2-OT	ENST00000493116.6	TSL:4	n.333+88705A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.867 AC: 131638 AN: 151778 Hom.: 57190 Cov.: 30

Gnomad AFR AF: 0.836

Gnomad AMI AF: 0.942

Gnomad AMR AF: 0.901

Gnomad ASJ AF: 0.854

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.913

Gnomad FIN AF: 0.877

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.864

Gnomad OTH AF: 0.877

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

GnomAD4 genome AF: 0.867 AC: 131741 AN: 151896 Hom.: 57237 Cov.: 30 AF XY: 0.871 AC XY: 64657 AN XY: 74238

African (AFR) AF: 0.836 AC: 34574 AN: 41370

American (AMR) AF: 0.901 AC: 13747 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.854 AC: 2965 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5159 AN: 5164

South Asian (SAS) AF: 0.912 AC: 4383 AN: 4804

European-Finnish (FIN) AF: 0.877 AC: 9264 AN: 10568

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.864 AC: 58686 AN: 67950

Other (OTH) AF: 0.879 AC: 1854 AN: 2110

Alfa AF: 0.870 Hom.: 7451

Bravo AF: 0.870

Asia WGS AF: 0.957 AC: 3326 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.4
DANN	Benign	0.71
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs2718771; hg19: chr3-180982076;