rs10502066

Variant names:

• chr11-106241326-G-A
• rs10502066

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 0.11 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.188 AC: 7792 AN: 41484

American (AMR) AF: 0.0851 AC: 1299 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0858 AC: 298 AN: 3472

East Asian (EAS) AF: 0.00910 AC: 47 AN: 5164

South Asian (SAS) AF: 0.0970 AC: 468 AN: 4826

European-Finnish (FIN) AF: 0.123 AC: 1298 AN: 10592

Middle Eastern (MID) AF: 0.147 AC: 43 AN: 292

European-Non Finnish (NFE) AF: 0.0772 AC: 5248 AN: 68006

Other (OTH) AF: 0.104 AC: 219 AN: 2110

Alfa AF: 0.0947 Hom.: 115

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
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs10502066; hg19: chr11-106112053;