11-25159419-A-G

Variant names:

• chr11-25159419-A-G
• rs1584186

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 0.815 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.815 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

Gnomad4 AFR AF: 0.805

Gnomad4 AMR AF: 0.807

Gnomad4 ASJ AF: 0.805

Gnomad4 EAS AF: 0.986

Gnomad4 SAS AF: 0.888

Gnomad4 FIN AF: 0.844

Gnomad4 NFE AF: 0.804

Gnomad4 OTH AF: 0.792

Alfa AF: 0.803 Hom.: 64212

Bravo AF: 0.810

Asia WGS AF: 0.926 AC: 3219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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