11-15271187-A-G

Variant names:

• chr11-15271187-A-G
• rs163861

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 0.749 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.701 AC: 28954 AN: 41314

American (AMR) AF: 0.761 AC: 11598 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.825 AC: 2856 AN: 3462

East Asian (EAS) AF: 0.741 AC: 3796 AN: 5124

South Asian (SAS) AF: 0.810 AC: 3888 AN: 4800

European-Finnish (FIN) AF: 0.776 AC: 8172 AN: 10526

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.763 AC: 51774 AN: 67828

Other (OTH) AF: 0.761 AC: 1600 AN: 2102

Alfa AF: 0.702 Hom.: 2020

Bravo AF: 0.743

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.48
DANN	Benign	0.37
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs163861; hg19: chr11-15292733;