rs10502066

chr11-106241326-G-A

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 0.11 in 152,128 control chromosomes in the GnomAD database, including 1,122 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 0.11 (1122 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.586

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16709 AN: 152010 Hom.: 1109 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.0852

Gnomad ASJ AF: 0.0858

Gnomad EAS AF: 0.00908

Gnomad SAS AF: 0.0965

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.0772

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.110 AC: 16763 AN: 152128 Hom.: 1122 Cov.: 32 AF XY: 0.112 AC XY: 8318 AN XY: 74376

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.0851

Gnomad4 ASJ AF: 0.0858

Gnomad4 EAS AF: 0.00910

Gnomad4 SAS AF: 0.0970

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.0772

Gnomad4 OTH AF: 0.104

Alfa AF: 0.0914 Hom.: 106

Bravo AF: 0.111

Asia WGS AF: 0.0680 AC: 238 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.17
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10502066; hg19: chr11-106112053;