rs10965244

Variant names:

• chr9-22130390-A-T
• rs10965244

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 0.18 in 152,244 control chromosomes in the GnomAD database, including 2,821 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 0.18 (2821 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.254

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.224 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: 0.180 AC: 27451 AN: 152124 Hom.: 2822 Cov.: 33

Gnomad AFR AF: 0.0962

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.180 AC: 27463 AN: 152244 Hom.: 2821 Cov.: 33 AF XY: 0.179 AC XY: 13353 AN XY: 74428

Gnomad4 AFR AF: 0.0963

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.226

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.227

Gnomad4 OTH AF: 0.186

Alfa AF: 0.204 Hom.: 489

Bravo AF: 0.168

Asia WGS AF: 0.122 AC: 425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.1
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10965244; hg19: chr9-22130389;