rs9664222

Variant names:

• chr10-87578876-A-C
• rs9664222

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 0.838 in 152,052 control chromosomes in the GnomAD database, including 53,842 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 0.84 (53842 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.176

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.934 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: 0.838 AC: 127345 AN: 151934 Hom.: 53776 Cov.: 30

Gnomad AFR AF: 0.942

Gnomad AMI AF: 0.819

Gnomad AMR AF: 0.845

Gnomad ASJ AF: 0.907

Gnomad EAS AF: 0.764

Gnomad SAS AF: 0.871

Gnomad FIN AF: 0.792

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.835

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

GnomAD4 genome AF: 0.838 AC: 127467 AN: 152052 Hom.: 53842 Cov.: 30 AF XY: 0.838 AC XY: 62250 AN XY: 74298

Gnomad4 AFR AF: 0.942

Gnomad4 AMR AF: 0.845

Gnomad4 ASJ AF: 0.907

Gnomad4 EAS AF: 0.764

Gnomad4 SAS AF: 0.871

Gnomad4 FIN AF: 0.792

Gnomad4 NFE AF: 0.781

Gnomad4 OTH AF: 0.837

Alfa AF: 0.796 Hom.: 106408

Bravo AF: 0.845

Asia WGS AF: 0.833 AC: 2896 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	9.7
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9664222; hg19: chr10-89338633;