rs10965243

chr9-22130066-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 0.128 in 152,234 control chromosomes in the GnomAD database, including 1,596 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 0.13 (1596 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.402

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19532 AN: 152116 Hom.: 1591 Cov.: 33

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.0557

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0888

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.128 AC: 19558 AN: 152234 Hom.: 1596 Cov.: 33 AF XY: 0.130 AC XY: 9710 AN XY: 74428

Gnomad4 AFR AF: 0.184

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.0557

Gnomad4 EAS AF: 0.381

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.0887

Gnomad4 OTH AF: 0.118

Alfa AF: 0.0984 Hom.: 1046

Bravo AF: 0.134

Asia WGS AF: 0.246 AC: 857 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.3
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10965243; hg19: chr9-22130065;