rs10870158

Positions:

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

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 0.655 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.578

Gnomad4 AMR AF: 0.616

Gnomad4 ASJ AF: 0.708

Gnomad4 EAS AF: 0.812

Gnomad4 SAS AF: 0.772

Gnomad4 FIN AF: 0.637

Gnomad4 NFE AF: 0.688

Gnomad4 OTH AF: 0.677

Alfa AF: 0.680 Hom.: 34936

Bravo AF: 0.649

Asia WGS AF: 0.755 AC: 2624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10870158; hg19: chr9-139885820;