rs10511946

Variant names:

• chr9-38121303-G-A
• rs10511946

Your query was ambiguous. Multiple possible variants found:

• chr9-38121303-G-A
• chr9-38121303-G-C
• chr9-38121303-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 0.484 in 152,042 control chromosomes in the GnomAD database, including 18,853 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 0.48 (18853 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.723
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.574 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: 0.484 AC: 73600 AN: 151924 Hom.: 18849 Cov.: 32

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.579

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.484 AC: 73591 AN: 152042 Hom.: 18853 Cov.: 32 AF XY: 0.484 AC XY: 35974 AN XY: 74306

African (AFR) AF: 0.292 AC: 12105 AN: 41484

American (AMR) AF: 0.527 AC: 8038 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.571 AC: 1979 AN: 3468

East Asian (EAS) AF: 0.411 AC: 2121 AN: 5166

South Asian (SAS) AF: 0.512 AC: 2469 AN: 4824

European-Finnish (FIN) AF: 0.548 AC: 5794 AN: 10564

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.579 AC: 39349 AN: 67954

Other (OTH) AF: 0.491 AC: 1038 AN: 2112

Alfa AF: 0.552 Hom.: 5201

Bravo AF: 0.472

Asia WGS AF: 0.412 AC: 1429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.92
DANN	Benign	0.68
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs10511946; hg19: chr9-38121300;