rs10090710

Variant names:

• chr8-54895132-G-C
• rs10090710

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 0.804 in 152,010 control chromosomes in the GnomAD database, including 49,495 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 0.80 (49495 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.896 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: 0.804 AC: 122080 AN: 151892 Hom.: 49434 Cov.: 31

Gnomad AFR AF: 0.904

Gnomad AMI AF: 0.828

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.703

Gnomad EAS AF: 0.822

Gnomad SAS AF: 0.880

Gnomad FIN AF: 0.779

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.755

Gnomad OTH AF: 0.766

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

GnomAD4 genome AF: 0.804 AC: 122193 AN: 152010 Hom.: 49495 Cov.: 31 AF XY: 0.805 AC XY: 59793 AN XY: 74280

African (AFR) AF: 0.904 AC: 37504 AN: 41496

American (AMR) AF: 0.765 AC: 11663 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.703 AC: 2439 AN: 3470

East Asian (EAS) AF: 0.821 AC: 4215 AN: 5134

South Asian (SAS) AF: 0.880 AC: 4241 AN: 4822

European-Finnish (FIN) AF: 0.779 AC: 8246 AN: 10584

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.755 AC: 51293 AN: 67948

Other (OTH) AF: 0.765 AC: 1613 AN: 2108

Alfa AF: 0.778 Hom.: 5760

Bravo AF: 0.806

Asia WGS AF: 0.829 AC: 2883 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.2
DANN	Benign	0.39
PhyloP100		-0.011

Splicing

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

Other links and lift over

dbSNP: rs10090710; hg19: chr8-55807692;