rs9369226

Variant names:

• chr6-40702977-A-G
• rs9369226

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.358 AC: 14851 AN: 41476

American (AMR) AF: 0.717 AC: 10961 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.782 AC: 2713 AN: 3470

East Asian (EAS) AF: 0.613 AC: 3161 AN: 5160

South Asian (SAS) AF: 0.565 AC: 2722 AN: 4820

European-Finnish (FIN) AF: 0.843 AC: 8904 AN: 10568

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.805 AC: 54743 AN: 67982

Other (OTH) AF: 0.662 AC: 1396 AN: 2110

Alfa AF: 0.767 Hom.: 48462

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
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs9369226; hg19: chr6-40670716;