rs10119466

Variant names:

• chr9-96789343-A-G
• rs10119466

Your query was ambiguous. Multiple possible variants found:

• chr9-96789343-A-G
• chr9-96789343-A-T

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 0.134 in 152,162 control chromosomes in the GnomAD database, including 3,308 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 (3308 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.483

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.379 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: 0.133 AC: 20263 AN: 152042 Hom.: 3274 Cov.: 32

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0679

Gnomad ASJ AF: 0.0219

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.0704

Gnomad FIN AF: 0.0458

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0152

Gnomad OTH AF: 0.0912

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

GnomAD4 genome AF: 0.134 AC: 20340 AN: 152162 Hom.: 3308 Cov.: 32 AF XY: 0.134 AC XY: 9991 AN XY: 74404

Gnomad4 AFR AF: 0.384

Gnomad4 AMR AF: 0.0677

Gnomad4 ASJ AF: 0.0219

Gnomad4 EAS AF: 0.237

Gnomad4 SAS AF: 0.0698

Gnomad4 FIN AF: 0.0458

Gnomad4 NFE AF: 0.0151

Gnomad4 OTH AF: 0.0898

Alfa AF: 0.0761 Hom.: 281

Bravo AF: 0.147

Asia WGS AF: 0.132 AC: 457 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.8
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10119466; hg19: chr9-99551625;