rs10739150

Variant names:

• chr9-8176226-T-G
• rs10739150

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;