11-25159419-A-G

Variant names:

• chr11-25159419-A-G
• rs1584186

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 0.815 in 152,056 control chromosomes in the GnomAD database, including 50,685 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 0.82 (50685 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.963 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: 0.815 AC: 123901 AN: 151938 Hom.: 50651 Cov.: 31

Gnomad AFR AF: 0.806

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.807

Gnomad ASJ AF: 0.805

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.887

Gnomad FIN AF: 0.844

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.804

Gnomad OTH AF: 0.789

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

GnomAD4 genome AF: 0.815 AC: 123990 AN: 152056 Hom.: 50685 Cov.: 31 AF XY: 0.820 AC XY: 60973 AN XY: 74318

African (AFR) AF: 0.805 AC: 33367 AN: 41436

American (AMR) AF: 0.807 AC: 12330 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.805 AC: 2793 AN: 3470

East Asian (EAS) AF: 0.986 AC: 5065 AN: 5138

South Asian (SAS) AF: 0.888 AC: 4278 AN: 4820

European-Finnish (FIN) AF: 0.844 AC: 8937 AN: 10590

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.804 AC: 54649 AN: 68008

Other (OTH) AF: 0.792 AC: 1673 AN: 2112

Alfa AF: 0.803 Hom.: 81966

Bravo AF: 0.810

Asia WGS AF: 0.926 AC: 3219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.17
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs1584186; hg19: chr11-25180965; COSMIC: COSV66701007;