rs10818894

Positions:

• chr9-123933491-G-A

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 0.306 in 152,154 control chromosomes in the GnomAD database, including 9,566 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 0.31 (9566 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0930

ACMG classification

Verdict is Benign. Variant got -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 = 0.579 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: 0.306 AC: 46534 AN: 152036 Hom.: 9544 Cov.: 33

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.220

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.306 AC: 46624 AN: 152154 Hom.: 9566 Cov.: 33 AF XY: 0.307 AC XY: 22822 AN XY: 74394

Gnomad4 AFR AF: 0.586

Gnomad4 AMR AF: 0.234

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.188

Gnomad4 FIN AF: 0.281

Gnomad4 NFE AF: 0.188

Gnomad4 OTH AF: 0.273

Alfa AF: 0.203 Hom.: 5778

Bravo AF: 0.315

Asia WGS AF: 0.195 AC: 678 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.2
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10818894; hg19: chr9-126695770;