rs9366999

Positions:

• chr6-39234381-G-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;