rs10739150

chr9-8176226-T-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 0.709 in 151,982 control chromosomes in the GnomAD database, including 39,022 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 0.71 (39022 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.620

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.783 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: 0.710 AC: 107762 AN: 151866 Hom.: 39028 Cov.: 32

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.692

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.859

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.700

Gnomad FIN AF: 0.824

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.719

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

GnomAD4 genome AF: 0.709 AC: 107775 AN: 151982 Hom.: 39022 Cov.: 32 AF XY: 0.708 AC XY: 52614 AN XY: 74292

Gnomad4 AFR AF: 0.583

Gnomad4 AMR AF: 0.612

Gnomad4 ASJ AF: 0.859

Gnomad4 EAS AF: 0.637

Gnomad4 SAS AF: 0.699

Gnomad4 FIN AF: 0.824

Gnomad4 NFE AF: 0.788

Gnomad4 OTH AF: 0.713

Alfa AF: 0.771 Hom.: 76055

Bravo AF: 0.687

Asia WGS AF: 0.617 AC: 2145 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.68
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10739150; hg19: chr9-8176226;