rs17091905

Variant names:

• chr8-19992246-G-A
• rs17091905

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 0.165 in 152,054 control chromosomes in the GnomAD database, including 2,492 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 0.17 (2492 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25086 AN: 151936 Hom.: 2489 Cov.: 32

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.0988

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.165 AC: 25108 AN: 152054 Hom.: 2492 Cov.: 32 AF XY: 0.162 AC XY: 12051 AN XY: 74362

Gnomad4 AFR AF: 0.282

Gnomad4 AMR AF: 0.119

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.108

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.0988

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.149

Alfa AF: 0.134 Hom.: 2521

Bravo AF: 0.172

Asia WGS AF: 0.127 AC: 443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.0
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17091905; hg19: chr8-19849757;