rs10119556

Variant names:

• chr9-96789704-A-G
• rs10119556

Your query was ambiguous. Multiple possible variants found:

• chr9-96789704-A-G
• chr9-96789704-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 0.143 in 152,078 control chromosomes in the GnomAD database, including 3,528 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 0.14 (3528 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

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 (AFR) allele frequency at 95% confidence interval = 0.381 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: 0.143 AC: 21658 AN: 151960 Hom.: 3495 Cov.: 32

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0684

Gnomad ASJ AF: 0.0245

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0923

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0165

Gnomad OTH AF: 0.0976

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

GnomAD4 genome AF: 0.143 AC: 21730 AN: 152078 Hom.: 3528 Cov.: 32 AF XY: 0.146 AC XY: 10884 AN XY: 74326

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.0682

Gnomad4 ASJ AF: 0.0245

Gnomad4 EAS AF: 0.338

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.0923

Gnomad4 NFE AF: 0.0165

Gnomad4 OTH AF: 0.0966

Alfa AF: 0.0846 Hom.: 333

Bravo AF: 0.153

Asia WGS AF: 0.195 AC: 677 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	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10119556; hg19: chr9-99551986;