rs7610679

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SOX2-OT	ENST00000498731.6	n.3879C>T		non_coding_transcript_exon_variant	Exon 5 of 5	1
SOX2-OT	ENST00000596250.7	n.3892C>T		non_coding_transcript_exon_variant	Exon 2 of 2	5
SOX2-OT	ENST00000600801.7	n.4000C>T		non_coding_transcript_exon_variant	Exon 3 of 3	5

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

Gnomad4 ASJ exome AF: 1.00

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

Gnomad4 AFR AF: 0.659

Gnomad4 AMR AF: 0.686

Gnomad4 ASJ AF: 0.462

Gnomad4 EAS AF: 0.729

Gnomad4 SAS AF: 0.562

Gnomad4 FIN AF: 0.675

Gnomad4 NFE AF: 0.583

Gnomad4 OTH AF: 0.587

Alfa AF: 0.581 Hom.: 33741

Bravo AF: 0.628

Asia WGS AF: 0.640 AC: 2153 AN: 3368

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7610679; hg19: chr3-181460587;