rs9369240

Variant names:

• chr6-40842273-A-G
• rs9369240

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 0.0505 in 152,234 control chromosomes in the GnomAD database, including 280 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 0.051 (280 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.180

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0607 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: 0.0506 AC: 7690 AN: 152116 Hom.: 280 Cov.: 32

Gnomad AFR AF: 0.0119

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.0291

Gnomad ASJ AF: 0.0899

Gnomad EAS AF: 0.0545

Gnomad SAS AF: 0.0226

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0622

Gnomad OTH AF: 0.0540

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

GnomAD4 genome AF: 0.0505 AC: 7690 AN: 152234 Hom.: 280 Cov.: 32 AF XY: 0.0532 AC XY: 3957 AN XY: 74424

Gnomad4 AFR AF: 0.0119

Gnomad4 AMR AF: 0.0290

Gnomad4 ASJ AF: 0.0899

Gnomad4 EAS AF: 0.0548

Gnomad4 SAS AF: 0.0222

Gnomad4 FIN AF: 0.144

Gnomad4 NFE AF: 0.0622

Gnomad4 OTH AF: 0.0549

Alfa AF: 0.0572 Hom.: 123

Bravo AF: 0.0424

Asia WGS AF: 0.0350 AC: 121 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.0
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: rs9369240; hg19: chr6-40810012;