rs10870158

Variant names:

• chr9-136991368-C-A
• rs10870158

Your query was ambiguous. Multiple possible variants found:

• chr9-136991368-C-A
• chr9-136991368-C-G

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 0.655 in 152,144 control chromosomes in the GnomAD database, including 32,892 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 0.65 (32892 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.927
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.791 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: 0.655 AC: 99563 AN: 152026 Hom.: 32884 Cov.: 34

Gnomad AFR AF: 0.579

Gnomad AMI AF: 0.730

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.812

Gnomad SAS AF: 0.773

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.673

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

GnomAD4 genome AF: 0.655 AC: 99605 AN: 152144 Hom.: 32892 Cov.: 34 AF XY: 0.656 AC XY: 48791 AN XY: 74378

African (AFR) AF: 0.578 AC: 24001 AN: 41502

American (AMR) AF: 0.616 AC: 9419 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.708 AC: 2459 AN: 3472

East Asian (EAS) AF: 0.812 AC: 4207 AN: 5182

South Asian (SAS) AF: 0.772 AC: 3724 AN: 4822

European-Finnish (FIN) AF: 0.637 AC: 6740 AN: 10580

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.688 AC: 46765 AN: 67972

Other (OTH) AF: 0.677 AC: 1432 AN: 2116

Alfa AF: 0.679 Hom.: 42230

Bravo AF: 0.649

Asia WGS AF: 0.755 AC: 2624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.1
DANN	Benign	0.80
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs10870158; hg19: chr9-139885820;