rs1558798

Positions:

• chr3-181749188-G-T

Variant summary

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

The variant allele was found at a frequency of 0.418 in 152,046 control chromosomes in the GnomAD database, including 13,586 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 0.42 (13586 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0560

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.181749188G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SOX2-OT	ENST00000498226.5	n.287-41485G>T		intron_variant		4
SOX2-OT	ENST00000593330.1	n.44+49305G>T		intron_variant		3
SOX2-OT	ENST00000595084.3	n.286+49305G>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63437 AN: 151926 Hom.: 13581 Cov.: 33

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.418 AC: 63489 AN: 152046 Hom.: 13586 Cov.: 33 AF XY: 0.423 AC XY: 31440 AN XY: 74316

Gnomad4 AFR AF: 0.490

Gnomad4 AMR AF: 0.442

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.506

Gnomad4 SAS AF: 0.419

Gnomad4 FIN AF: 0.484

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.375

Alfa AF: 0.373 Hom.: 12949

Bravo AF: 0.423

Asia WGS AF: 0.463 AC: 1611 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1558798; hg19: chr3-181466976;