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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.292

Gnomad4 AMR AF: 0.527

Gnomad4 ASJ AF: 0.571

Gnomad4 EAS AF: 0.411

Gnomad4 SAS AF: 0.512

Gnomad4 FIN AF: 0.548

Gnomad4 NFE AF: 0.579

Gnomad4 OTH AF: 0.491

Alfa AF: 0.559 Hom.: 5176

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10511946; hg19: chr9-38121300;