11-26748089-T-G

Position:

• chr11-26748089-T-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 0.349 in 151,336 control chromosomes in the GnomAD database, including 11,582 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 0.35 (11582 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.415

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.350 AC: 52872 AN: 151214 Hom.: 11584 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.00544

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.349 AC: 52863 AN: 151336 Hom.: 11582 Cov.: 32 AF XY: 0.350 AC XY: 25859 AN XY: 73922

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.472

Gnomad4 EAS AF: 0.00545

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.563

Gnomad4 NFE AF: 0.485

Gnomad4 OTH AF: 0.390

Alfa AF: 0.447 Hom.: 20826

Bravo AF: 0.320

Asia WGS AF: 0.143 AC: 499 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	10
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10501068; hg19: chr11-26769636;