3-181698818-T-G

Position:

• chr3-181698818-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000654649.1(SOX2-OT):​n.9T>G 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 0.617 in 151,436 control chromosomes in the GnomAD database, including 30,833 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 (30831 hom., cov: 29)
  • Exomes 𝑓: 0.38 (2 hom.)
• Consequence: SOX2-OT ENST00000654649.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.617

Genes affected

SOX2-OT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SOX2-OT	NR_004053.3	n.482-780T>G		intron_variant
SOX2-OT	NR_075089.1	n.482-780T>G		intron_variant
SOX2-OT	NR_075090.1	n.482-40751T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SOX2-OT	ENST00000476964.6	n.482-40751T>G		intron_variant		1
SOX2-OT	ENST00000491282.6	n.308-780T>G		intron_variant		1
SOX2-OT	ENST00000498731.6	n.255-780T>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.617 AC: 93378 AN: 151294 Hom.: 30786 Cov.: 29

Gnomad AFR AF: 0.850

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.561

GnomAD4 exome AF: 0.385 AC: 10 AN: 26 Hom.: 2 Cov.: 0 AF XY: 0.278 AC XY: 5 AN XY: 18

Gnomad4 AFR exome AF: 1.00

Gnomad4 EAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.350

GnomAD4 genome AF: 0.617 AC: 93485 AN: 151410 Hom.: 30831 Cov.: 29 AF XY: 0.612 AC XY: 45271 AN XY: 73916

Gnomad4 AFR AF: 0.851

Gnomad4 AMR AF: 0.579

Gnomad4 ASJ AF: 0.449

Gnomad4 EAS AF: 0.757

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.549

Gnomad4 NFE AF: 0.520

Gnomad4 OTH AF: 0.560

Alfa AF: 0.517 Hom.: 17186

Bravo AF: 0.639

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	13
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13070015; hg19: chr3-181416606;