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. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.384 AC: 15927 AN: 41440

American (AMR) AF: 0.0677 AC: 1036 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0219 AC: 76 AN: 3472

East Asian (EAS) AF: 0.237 AC: 1225 AN: 5174

South Asian (SAS) AF: 0.0698 AC: 337 AN: 4826

European-Finnish (FIN) AF: 0.0458 AC: 486 AN: 10614

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0151 AC: 1030 AN: 68018

Other (OTH) AF: 0.0898 AC: 190 AN: 2116

Alfa AF: 0.0848 Hom.: 328

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
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs10119466; hg19: chr9-99551625;