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. The variant received -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
• Publications: 80 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0915 AC: 3800 AN: 41530

American (AMR) AF: 0.389 AC: 5931 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1339 AN: 3470

East Asian (EAS) AF: 0.616 AC: 3181 AN: 5162

South Asian (SAS) AF: 0.397 AC: 1914 AN: 4822

European-Finnish (FIN) AF: 0.318 AC: 3369 AN: 10578

Middle Eastern (MID) AF: 0.377 AC: 110 AN: 292

European-Non Finnish (NFE) AF: 0.387 AC: 26297 AN: 67948

Other (OTH) AF: 0.343 AC: 720 AN: 2100

Alfa AF: 0.186 Hom.: 550

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
PhyloP100		-0.042

Splicing

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

Other links and lift over

dbSNP: rs10759931; hg19: chr9-120464147;