rs9366999

Variant names:

• chr6-39234381-G-A
• rs9366999

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 0.316 in 151,598 control chromosomes in the GnomAD database, including 8,420 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 0.32 (8420 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0670

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.72 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: 0.316 AC: 47938 AN: 151496 Hom.: 8401 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.316 AC: 47978 AN: 151598 Hom.: 8420 Cov.: 32 AF XY: 0.329 AC XY: 24377 AN XY: 74072

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.340

Gnomad4 EAS AF: 0.740

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.443

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.351

Alfa AF: 0.307 Hom.: 12548

Bravo AF: 0.312

Asia WGS AF: 0.510 AC: 1772 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	8.4
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9366999; hg19: chr6-39202157;