chr3-181279171-C-T

Variant names:

• chr3-181279171-C-T
• rs7619173
• ENST00000460739.6:n.213+103588C>T

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+103588C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 151,982 control chromosomes in the GnomAD database, including 21,001 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 0.48 (21001 hom., cov: 33)
• Consequence: SOX2-OT ENST00000460739.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.120
• Publications: 8 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.81 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+103588C>T		intron	N/A
	SOX2-OT	NR_075092.1		n.218+103588C>T		intron	N/A
	SOX2-OT	NR_075093.1		n.194+103588C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SOX2-OT	ENST00000460739.6	TSL:4	n.213+103588C>T		intron	N/A
	SOX2-OT	ENST00000469278.5	TSL:4	n.194+103588C>T		intron	N/A
	SOX2-OT	ENST00000493116.6	TSL:4	n.333+103588C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72870 AN: 151864 Hom.: 20939 Cov.: 33

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.480 AC: 72993 AN: 151982 Hom.: 21001 Cov.: 33 AF XY: 0.470 AC XY: 34905 AN XY: 74312

African (AFR) AF: 0.817 AC: 33899 AN: 41498

American (AMR) AF: 0.359 AC: 5490 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1493 AN: 3468

East Asian (EAS) AF: 0.262 AC: 1360 AN: 5182

South Asian (SAS) AF: 0.432 AC: 2080 AN: 4816

European-Finnish (FIN) AF: 0.273 AC: 2886 AN: 10572

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.358 AC: 24301 AN: 67856

Other (OTH) AF: 0.481 AC: 1016 AN: 2112

Alfa AF: 0.386 Hom.: 14766

Bravo AF: 0.498

Asia WGS AF: 0.440 AC: 1527 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.6
DANN	Benign	0.38
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs7619173; hg19: chr3-180996959;