rs10119466

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;