chr3-181742799-C-T

Variant names:

• chr3-181742799-C-T
• rs7610679
• ENST00000498731.6:n.3879C>T

Variant summary

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

The ENST00000498731.6(SOX2-OT):​n.3879C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.62 in 141,980 control chromosomes in the GnomAD database, including 27,584 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 0.62 (27583 hom., cov: 21)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: SOX2-OT ENST00000498731.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180
• Publications: 9 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=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000498731.6. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SOX2-OT	ENST00000498731.6	TSL:1	n.3879C>T		non_coding_transcript_exon	Exon 5 of 5
	SOX2-OT	ENST00000596250.7	TSL:5	n.3892C>T		non_coding_transcript_exon	Exon 2 of 2
	SOX2-OT	ENST00000600801.7	TSL:5	n.4000C>T		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.620 AC: 87979 AN: 141886 Hom.: 27549 Cov.: 21

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.730

Gnomad SAS AF: 0.562

Gnomad FIN AF: 0.675

Gnomad MID AF: 0.461

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.582

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.620 AC: 88054 AN: 141978 Hom.: 27583 Cov.: 21 AF XY: 0.624 AC XY: 42962 AN XY: 68810

African (AFR) AF: 0.659 AC: 24625 AN: 37358

American (AMR) AF: 0.686 AC: 9660 AN: 14090

Ashkenazi Jewish (ASJ) AF: 0.462 AC: 1559 AN: 3372

East Asian (EAS) AF: 0.729 AC: 3499 AN: 4800

South Asian (SAS) AF: 0.562 AC: 2481 AN: 4414

European-Finnish (FIN) AF: 0.675 AC: 6165 AN: 9138

Middle Eastern (MID) AF: 0.466 AC: 122 AN: 262

European-Non Finnish (NFE) AF: 0.583 AC: 38351 AN: 65754

Other (OTH) AF: 0.587 AC: 1119 AN: 1906

Alfa AF: 0.587 Hom.: 43516

Bravo AF: 0.628

Asia WGS AF: 0.640 AC: 2153 AN: 3368

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	5.2
DANN	Benign	0.88
PhyloP100		-0.018

Splicing

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

Other links and lift over

dbSNP: rs7610679; hg19: chr3-181460587;