rs561655

Positions:

• chr11-86089237-G-A
• chr11-86089237-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.693 in 152,090 control chromosomes in the GnomAD database, including 37,164 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 0.69 (37164 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.826 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.693 AC: 105339 AN: 151972 Hom.: 37131 Cov.: 31

Gnomad AFR AF: 0.834

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.605

Gnomad NFE AF: 0.655

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.693 AC: 105430 AN: 152090 Hom.: 37164 Cov.: 31 AF XY: 0.688 AC XY: 51136 AN XY: 74320

Gnomad4 AFR AF: 0.833

Gnomad4 AMR AF: 0.646

Gnomad4 ASJ AF: 0.646

Gnomad4 EAS AF: 0.505

Gnomad4 SAS AF: 0.579

Gnomad4 FIN AF: 0.630

Gnomad4 NFE AF: 0.655

Gnomad4 OTH AF: 0.687

Alfa AF: 0.652 Hom.: 56782

Bravo AF: 0.699

Asia WGS AF: 0.561 AC: 1952 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	16
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs561655; hg19: chr11-85800279;