rs10965245

Variant names:

• chr9-22130516-G-A
• rs10965245

Your query was ambiguous. Multiple possible variants found:

• chr9-22130516-G-A
• chr9-22130516-G-C

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 0.125 in 151,996 control chromosomes in the GnomAD database, including 1,549 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 (1549 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.125 AC: 19033 AN: 151878 Hom.: 1544 Cov.: 33

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0522

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.0987

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0848

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.125 AC: 19059 AN: 151996 Hom.: 1549 Cov.: 33 AF XY: 0.127 AC XY: 9461 AN XY: 74284

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.0522

Gnomad4 EAS AF: 0.381

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.0987

Gnomad4 NFE AF: 0.0847

Gnomad4 OTH AF: 0.115

Alfa AF: 0.0955 Hom.: 331

Bravo AF: 0.131

Asia WGS AF: 0.246 AC: 855 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.1
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10965245; hg19: chr9-22130515;