rs10115769

Variant names:

• chr9-108634462-G-A
• rs10115769

Your query was ambiguous. Multiple possible variants found:

• chr9-108634462-G-A
• chr9-108634462-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 0.138 in 152,118 control chromosomes in the GnomAD database, including 1,852 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 0.14 (1852 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.508
• Publications: 0 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 (AFR) allele frequency at 95% confidence interval = 0.246 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: 0.138 AC: 20983 AN: 152000 Hom.: 1845 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.0766

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.0643

Gnomad FIN AF: 0.0787

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0954

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.138 AC: 21014 AN: 152118 Hom.: 1852 Cov.: 32 AF XY: 0.135 AC XY: 10055 AN XY: 74368

African (AFR) AF: 0.250 AC: 10383 AN: 41478

American (AMR) AF: 0.108 AC: 1650 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0766 AC: 266 AN: 3472

East Asian (EAS) AF: 0.129 AC: 665 AN: 5166

South Asian (SAS) AF: 0.0656 AC: 316 AN: 4818

European-Finnish (FIN) AF: 0.0787 AC: 834 AN: 10594

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0954 AC: 6485 AN: 67976

Other (OTH) AF: 0.129 AC: 272 AN: 2112

Alfa AF: 0.103 Hom.: 2088

Bravo AF: 0.146

Asia WGS AF: 0.111 AC: 386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.8
DANN	Benign	0.67
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs10115769; hg19: chr9-111396742;