11-134870879-G-T

Variant names:

• chr11-134870879-G-T
• rs11224052

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 0.266 in 150,284 control chromosomes in the GnomAD database, including 5,299 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 0.27 (5299 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.262
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.27 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: 0.266 AC: 39921 AN: 150178 Hom.: 5286 Cov.: 31

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.266 AC: 39969 AN: 150284 Hom.: 5299 Cov.: 31 AF XY: 0.266 AC XY: 19523 AN XY: 73308

African (AFR) AF: 0.273 AC: 11183 AN: 40926

American (AMR) AF: 0.237 AC: 3597 AN: 15148

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 536 AN: 3458

East Asian (EAS) AF: 0.246 AC: 1256 AN: 5112

South Asian (SAS) AF: 0.264 AC: 1254 AN: 4758

European-Finnish (FIN) AF: 0.284 AC: 2834 AN: 9986

Middle Eastern (MID) AF: 0.219 AC: 64 AN: 292

European-Non Finnish (NFE) AF: 0.273 AC: 18488 AN: 67614

Other (OTH) AF: 0.239 AC: 500 AN: 2088

Alfa AF: 0.171 Hom.: 337

Bravo AF: 0.264

Asia WGS AF: 0.245 AC: 851 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.11
DANN	Benign	0.32
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs11224052; hg19: chr11-134740773;