rs10501784

Variant names:

• chr11-92219378-A-G
• rs10501784

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 0.787 in 152,172 control chromosomes in the GnomAD database, including 47,332 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 0.79 (47332 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.237

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.826 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: 0.787 AC: 119721 AN: 152054 Hom.: 47284 Cov.: 33

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.866

Gnomad AMR AF: 0.837

Gnomad ASJ AF: 0.802

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.837

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.844

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.789

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

GnomAD4 genome AF: 0.787 AC: 119827 AN: 152172 Hom.: 47332 Cov.: 33 AF XY: 0.784 AC XY: 58340 AN XY: 74368

Gnomad4 AFR AF: 0.812

Gnomad4 AMR AF: 0.838

Gnomad4 ASJ AF: 0.802

Gnomad4 EAS AF: 0.617

Gnomad4 SAS AF: 0.838

Gnomad4 FIN AF: 0.708

Gnomad4 NFE AF: 0.781

Gnomad4 OTH AF: 0.789

Alfa AF: 0.779 Hom.: 10231

Bravo AF: 0.795

Asia WGS AF: 0.742 AC: 2581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.2
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10501784; hg19: chr11-91952544;