rs9905258

chr17-6003941-A-G

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 0.394 in 152,038 control chromosomes in the GnomAD database, including 12,697 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 0.39 (12697 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.586

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59841 AN: 151920 Hom.: 12694 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.394 AC: 59869 AN: 152038 Hom.: 12697 Cov.: 32 AF XY: 0.394 AC XY: 29307 AN XY: 74316

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.431

Gnomad4 ASJ AF: 0.413

Gnomad4 EAS AF: 0.556

Gnomad4 SAS AF: 0.445

Gnomad4 FIN AF: 0.440

Gnomad4 NFE AF: 0.463

Gnomad4 OTH AF: 0.408

Alfa AF: 0.425 Hom.: 2383

Bravo AF: 0.389

Asia WGS AF: 0.534 AC: 1855 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.0
Dann	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9905258; hg19: chr17-5907261; COSMIC: COSV73818336;