rs478881

Positions:

• chr11-134269886-A-G
• chr11-134269886-A-T

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 0.625 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.134269886A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.732

Gnomad4 AMR AF: 0.627

Gnomad4 ASJ AF: 0.642

Gnomad4 EAS AF: 0.452

Gnomad4 SAS AF: 0.548

Gnomad4 FIN AF: 0.499

Gnomad4 NFE AF: 0.573

Gnomad4 OTH AF: 0.626

Alfa AF: 0.737 Hom.: 59034

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs478881; hg19: chr11-134139780;