rs17810889

Positions:

• chr8-11765727-A-G
• chr8-11765727-A-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 0.285 in 152,214 control chromosomes in the GnomAD database, including 6,311 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 0.28 (6311 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.155

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.11765727A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43275 AN: 152096 Hom.: 6303 Cov.: 33

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.285 AC: 43323 AN: 152214 Hom.: 6311 Cov.: 33 AF XY: 0.282 AC XY: 21017 AN XY: 74432

Gnomad4 AFR AF: 0.244

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.417

Gnomad4 EAS AF: 0.233

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.306

Gnomad4 OTH AF: 0.316

Alfa AF: 0.230 Hom.: 825

Bravo AF: 0.288

Asia WGS AF: 0.290 AC: 1009 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.5
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17810889; hg19: chr8-11623236;