rs10989329

Positions:

• chr9-100952798-A-G

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 0.0105 in 152,162 control chromosomes in the GnomAD database, including 30 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 0.011 (30 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0695 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: 0.0106 AC: 1607 AN: 152044 Hom.: 30 Cov.: 31

Gnomad AFR AF: 0.00212

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0262

Gnomad ASJ AF: 0.0179

Gnomad EAS AF: 0.0759

Gnomad SAS AF: 0.0157

Gnomad FIN AF: 0.00132

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00793

Gnomad OTH AF: 0.0153

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

GnomAD4 genome AF: 0.0105 AC: 1605 AN: 152162 Hom.: 30 Cov.: 31 AF XY: 0.0105 AC XY: 780 AN XY: 74408

Gnomad4 AFR AF: 0.00212

Gnomad4 AMR AF: 0.0261

Gnomad4 ASJ AF: 0.0179

Gnomad4 EAS AF: 0.0756

Gnomad4 SAS AF: 0.0156

Gnomad4 FIN AF: 0.00132

Gnomad4 NFE AF: 0.00793

Gnomad4 OTH AF: 0.0151

Alfa AF: 0.0110 Hom.: 25

Bravo AF: 0.0134

Asia WGS AF: 0.0420 AC: 145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.0
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10989329; hg19: chr9-103715080;