3-181486314-G-T

Position:

• chr3-181486314-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000493521.5(SOX2-OT):​n.219-77406G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.434 in 151,310 control chromosomes in the GnomAD database, including 15,397 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 0.43 (15397 hom., cov: 30)
• Consequence: SOX2-OT ENST00000493521.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0300

Genes affected

SOX2-OT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SOX2-OT	NR_075091.1	n.219-77406G>T		intron_variant
SOX2-OT	NR_075092.1	n.219-77406G>T		intron_variant
SOX2-OT	NR_075093.1	n.195-77406G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SOX2-OT	ENST00000460739.5	n.214-77406G>T		intron_variant		4
SOX2-OT	ENST00000469278.5	n.195-77406G>T		intron_variant		4
SOX2-OT	ENST00000493116.6	n.334-77406G>T		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65691 AN: 151190 Hom.: 15383 Cov.: 30

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.434 AC: 65725 AN: 151310 Hom.: 15397 Cov.: 30 AF XY: 0.435 AC XY: 32149 AN XY: 73864

Gnomad4 AFR AF: 0.249

Gnomad4 AMR AF: 0.509

Gnomad4 ASJ AF: 0.453

Gnomad4 EAS AF: 0.451

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.525

Gnomad4 NFE AF: 0.515

Gnomad4 OTH AF: 0.434

Alfa AF: 0.484 Hom.: 22264

Bravo AF: 0.421

Asia WGS AF: 0.467 AC: 1625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	5.7
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2199718; hg19: chr3-181204102;