rs10759931

Variant names:

• chr9-117701869-G-A
• rs10759931

Your query was ambiguous. Multiple possible variants found:

• chr9-117701869-G-A
• chr9-117701869-G-C
• chr9-117701869-G-T

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 0.309 in 152,080 control chromosomes in the GnomAD database, including 8,882 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 0.31 (8882 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0420

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.598 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: 0.310 AC: 47049 AN: 151962 Hom.: 8887 Cov.: 32

Gnomad AFR AF: 0.0917

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.309 AC: 47048 AN: 152080 Hom.: 8882 Cov.: 32 AF XY: 0.311 AC XY: 23132 AN XY: 74336

Gnomad4 AFR AF: 0.0915

Gnomad4 AMR AF: 0.389

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.616

Gnomad4 SAS AF: 0.397

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.343

Alfa AF: 0.191 Hom.: 545

Bravo AF: 0.308

Asia WGS AF: 0.489 AC: 1700 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.3
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10759931; hg19: chr9-120464147;