11-134269886-A-G

Variant names:

• chr11-134269886-A-G
• rs478881

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 0.625 in 120,290 control chromosomes in the GnomAD database, including 20,007 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 0.63 (20007 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.725 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: 0.625 AC: 75096 AN: 120172 Hom.: 19968 Cov.: 28

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.499

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.627

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

GnomAD4 genome AF: 0.625 AC: 75193 AN: 120290 Hom.: 20007 Cov.: 28 AF XY: 0.624 AC XY: 36371 AN XY: 58288

African (AFR) AF: 0.732 AC: 29316 AN: 40062

American (AMR) AF: 0.627 AC: 7430 AN: 11856

Ashkenazi Jewish (ASJ) AF: 0.642 AC: 1859 AN: 2894

East Asian (EAS) AF: 0.452 AC: 1398 AN: 3090

South Asian (SAS) AF: 0.548 AC: 1819 AN: 3322

European-Finnish (FIN) AF: 0.499 AC: 3395 AN: 6808

Middle Eastern (MID) AF: 0.571 AC: 136 AN: 238

European-Non Finnish (NFE) AF: 0.573 AC: 28456 AN: 49704

Other (OTH) AF: 0.626 AC: 1056 AN: 1688

Alfa AF: 0.742 Hom.: 101745

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.90
DANN	Benign	0.098
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs478881; hg19: chr11-134139780;