rs9369226

Positions:

• chr6-40702977-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 0.661 in 152,078 control chromosomes in the GnomAD database, including 36,084 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 0.66 (36084 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.144

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 = 0.8 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: 0.661 AC: 100417 AN: 151960 Hom.: 36068 Cov.: 32

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.867

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.782

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.843

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.805

Gnomad OTH AF: 0.660

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

GnomAD4 genome AF: 0.661 AC: 100454 AN: 152078 Hom.: 36084 Cov.: 32 AF XY: 0.661 AC XY: 49121 AN XY: 74350

Gnomad4 AFR AF: 0.358

Gnomad4 AMR AF: 0.717

Gnomad4 ASJ AF: 0.782

Gnomad4 EAS AF: 0.613

Gnomad4 SAS AF: 0.565

Gnomad4 FIN AF: 0.843

Gnomad4 NFE AF: 0.805

Gnomad4 OTH AF: 0.662

Alfa AF: 0.765 Hom.: 30575

Bravo AF: 0.643

Asia WGS AF: 0.567 AC: 1970 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	0.25
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9369226; hg19: chr6-40670716;