rs10119556

chr9-96789704-A-Gchr9-96789704-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;