3-181194230-C-G

Variant names:

• chr3-181194230-C-G
• rs2567661
• ENST00000460739.6:n.213+18647C>G

Variant summary

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

The ENST00000493521.5(SOX2-OT):​n.218+18647C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.768 in 152,040 control chromosomes in the GnomAD database, including 46,138 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 0.77 (46138 hom., cov: 31)
• Consequence: SOX2-OT ENST00000493521.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.914
• 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 (NFE) allele frequency at 95% confidence interval = 0.85 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000493521.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SOX2-OT	NR_075091.1		n.218+18647C>G		intron	N/A
	SOX2-OT	NR_075092.1		n.218+18647C>G		intron	N/A
	SOX2-OT	NR_075093.1		n.194+18647C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SOX2-OT	ENST00000460739.6	TSL:4	n.213+18647C>G		intron	N/A
	SOX2-OT	ENST00000469278.5	TSL:4	n.194+18647C>G		intron	N/A
	SOX2-OT	ENST00000493116.6	TSL:4	n.333+18647C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.768 AC: 116678 AN: 151922 Hom.: 46109 Cov.: 31

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.950

Gnomad AMR AF: 0.791

Gnomad ASJ AF: 0.839

Gnomad EAS AF: 0.853

Gnomad SAS AF: 0.805

Gnomad FIN AF: 0.872

Gnomad MID AF: 0.742

Gnomad NFE AF: 0.856

Gnomad OTH AF: 0.785

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

GnomAD4 genome AF: 0.768 AC: 116750 AN: 152040 Hom.: 46138 Cov.: 31 AF XY: 0.771 AC XY: 57315 AN XY: 74350

African (AFR) AF: 0.563 AC: 23306 AN: 41390

American (AMR) AF: 0.791 AC: 12088 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.839 AC: 2912 AN: 3472

East Asian (EAS) AF: 0.853 AC: 4407 AN: 5168

South Asian (SAS) AF: 0.804 AC: 3873 AN: 4816

European-Finnish (FIN) AF: 0.872 AC: 9244 AN: 10596

Middle Eastern (MID) AF: 0.750 AC: 219 AN: 292

European-Non Finnish (NFE) AF: 0.856 AC: 58184 AN: 68010

Other (OTH) AF: 0.786 AC: 1654 AN: 2104

Alfa AF: 0.814 Hom.: 6037

Bravo AF: 0.755

Asia WGS AF: 0.828 AC: 2880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.23
DANN	Benign	0.46
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs2567661; hg19: chr3-180912018;