11-25940552-A-G

Position:

• chr11-25940552-A-G

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 0.0642 in 152,268 control chromosomes in the GnomAD database, including 617 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 0.064 (617 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.512

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0641 AC: 9760 AN: 152150 Hom.: 615 Cov.: 33

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.0369

Gnomad ASJ AF: 0.0605

Gnomad EAS AF: 0.0377

Gnomad SAS AF: 0.0513

Gnomad FIN AF: 0.00962

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0200

Gnomad OTH AF: 0.0568

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

GnomAD4 genome AF: 0.0642 AC: 9773 AN: 152268 Hom.: 617 Cov.: 33 AF XY: 0.0625 AC XY: 4655 AN XY: 74454

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.0369

Gnomad4 ASJ AF: 0.0605

Gnomad4 EAS AF: 0.0376

Gnomad4 SAS AF: 0.0513

Gnomad4 FIN AF: 0.00962

Gnomad4 NFE AF: 0.0200

Gnomad4 OTH AF: 0.0562

Alfa AF: 0.0465 Hom.: 56

Bravo AF: 0.0690

Asia WGS AF: 0.0420 AC: 145 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.4
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10501029; hg19: chr11-25962099;