11-15271187-A-G

Variant names:

• chr11-15271187-A-G
• rs163861

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 0.749 in 151,590 control chromosomes in the GnomAD database, including 42,762 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 0.75 (42762 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.789 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: 0.749 AC: 113497 AN: 151472 Hom.: 42736 Cov.: 28

Gnomad AFR AF: 0.701

Gnomad AMI AF: 0.771

Gnomad AMR AF: 0.761

Gnomad ASJ AF: 0.825

Gnomad EAS AF: 0.742

Gnomad SAS AF: 0.809

Gnomad FIN AF: 0.776

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.763

Gnomad OTH AF: 0.763

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

GnomAD4 genome AF: 0.749 AC: 113585 AN: 151590 Hom.: 42762 Cov.: 28 AF XY: 0.749 AC XY: 55485 AN XY: 74074

Gnomad4 AFR AF: 0.701

Gnomad4 AMR AF: 0.761

Gnomad4 ASJ AF: 0.825

Gnomad4 EAS AF: 0.741

Gnomad4 SAS AF: 0.810

Gnomad4 FIN AF: 0.776

Gnomad4 NFE AF: 0.763

Gnomad4 OTH AF: 0.761

Alfa AF: 0.702 Hom.: 2020

Bravo AF: 0.743

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.48
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs163861; hg19: chr11-15292733;