rs10099863

Variant names:

• chr8-97862465-A-C
• rs10099863

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 0.721 in 151,990 control chromosomes in the GnomAD database, including 41,162 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 0.72 (41162 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.866
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.841 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.721 AC: 109554 AN: 151870 Hom.: 41152 Cov.: 31

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.831

Gnomad AMR AF: 0.747

Gnomad ASJ AF: 0.790

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.744

Gnomad MID AF: 0.752

Gnomad NFE AF: 0.846

Gnomad OTH AF: 0.744

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

GnomAD4 genome AF: 0.721 AC: 109610 AN: 151990 Hom.: 41162 Cov.: 31 AF XY: 0.712 AC XY: 52903 AN XY: 74296

African (AFR) AF: 0.546 AC: 22620 AN: 41432

American (AMR) AF: 0.746 AC: 11382 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.790 AC: 2743 AN: 3470

East Asian (EAS) AF: 0.405 AC: 2093 AN: 5170

South Asian (SAS) AF: 0.594 AC: 2862 AN: 4820

European-Finnish (FIN) AF: 0.744 AC: 7844 AN: 10550

Middle Eastern (MID) AF: 0.750 AC: 219 AN: 292

European-Non Finnish (NFE) AF: 0.846 AC: 57543 AN: 67986

Other (OTH) AF: 0.735 AC: 1546 AN: 2104

Alfa AF: 0.804 Hom.: 93777

Bravo AF: 0.716

Asia WGS AF: 0.467 AC: 1629 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	3.2
DANN	Benign	0.71
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs10099863; hg19: chr8-98874693; COSMIC: COSV72272114;