rs10984642

Variant names:

• chr9-119688062-C-T
• rs10984642

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 0.126 in 152,164 control chromosomes in the GnomAD database, including 1,288 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 (1288 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.184

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.18 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: 0.126 AC: 19216 AN: 152048 Hom.: 1290 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.0933

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.126 AC: 19220 AN: 152164 Hom.: 1288 Cov.: 32 AF XY: 0.126 AC XY: 9361 AN XY: 74366

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.0931

Gnomad4 ASJ AF: 0.189

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.190

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.108

Alfa AF: 0.129 Hom.: 745

Bravo AF: 0.124

Asia WGS AF: 0.0800 AC: 278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.2
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10984642; hg19: chr9-122450340;