rs10818894

Variant names:

• chr9-123933491-G-A
• rs10818894

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.586 AC: 24291 AN: 41478

American (AMR) AF: 0.234 AC: 3579 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 700 AN: 3468

East Asian (EAS) AF: 0.115 AC: 593 AN: 5176

South Asian (SAS) AF: 0.188 AC: 906 AN: 4824

European-Finnish (FIN) AF: 0.281 AC: 2972 AN: 10590

Middle Eastern (MID) AF: 0.219 AC: 64 AN: 292

European-Non Finnish (NFE) AF: 0.188 AC: 12807 AN: 68004

Other (OTH) AF: 0.273 AC: 578 AN: 2114

Alfa AF: 0.221 Hom.: 18477

Bravo AF: 0.315

Asia WGS AF: 0.195 AC: 678 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.2
DANN	Benign	0.38
PhyloP100		-0.093

Splicing

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

Other links and lift over

dbSNP: rs10818894; hg19: chr9-126695770;