rs9815059

Positions:

• chr3-81489477-C-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 0.294 in 151,744 control chromosomes in the GnomAD database, including 6,775 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 0.29 (6775 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.148

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.81489477C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44628 AN: 151626 Hom.: 6770 Cov.: 32

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.294 AC: 44676 AN: 151744 Hom.: 6775 Cov.: 32 AF XY: 0.291 AC XY: 21561 AN XY: 74146

Gnomad4 AFR AF: 0.360

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.427

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.274

Gnomad4 OTH AF: 0.278

Alfa AF: 0.293 Hom.: 597

Bravo AF: 0.303

Asia WGS AF: 0.291 AC: 1007 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.9
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9815059; hg19: chr3-81538628;