rs11029158

Variant names:

• chr11-26084092-C-T
• rs11029158

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 0.0652 in 152,020 control chromosomes in the GnomAD database, including 547 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 0.065 (547 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.144 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: 0.0650 AC: 9879 AN: 151902 Hom.: 540 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.0361

Gnomad ASJ AF: 0.0366

Gnomad EAS AF: 0.0287

Gnomad SAS AF: 0.0274

Gnomad FIN AF: 0.0276

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0345

Gnomad OTH AF: 0.0651

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

GnomAD4 genome AF: 0.0652 AC: 9908 AN: 152020 Hom.: 547 Cov.: 32 AF XY: 0.0641 AC XY: 4762 AN XY: 74290

African (AFR) AF: 0.147 AC: 6099 AN: 41478

American (AMR) AF: 0.0360 AC: 548 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.0366 AC: 127 AN: 3470

East Asian (EAS) AF: 0.0286 AC: 147 AN: 5138

South Asian (SAS) AF: 0.0270 AC: 130 AN: 4818

European-Finnish (FIN) AF: 0.0276 AC: 292 AN: 10590

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0345 AC: 2344 AN: 67978

Other (OTH) AF: 0.0644 AC: 136 AN: 2112

Alfa AF: 0.0527 Hom.: 60

Bravo AF: 0.0697

Asia WGS AF: 0.0450 AC: 157 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.55
DANN	Benign	0.81
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs11029158; hg19: chr11-26105639;