chr11-91554359-T-C

Position:

• chr11-91554359-T-C

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 0.591 in 151,958 control chromosomes in the GnomAD database, including 27,135 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 0.59 (27135 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.393

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 (EAS) allele frequency at 95% confidence interval = 0.787 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: 0.591 AC: 89783 AN: 151838 Hom.: 27100 Cov.: 32

Gnomad AFR AF: 0.667

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.522

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.591 AC: 89878 AN: 151958 Hom.: 27135 Cov.: 32 AF XY: 0.595 AC XY: 44171 AN XY: 74264

Gnomad4 AFR AF: 0.667

Gnomad4 AMR AF: 0.656

Gnomad4 ASJ AF: 0.529

Gnomad4 EAS AF: 0.808

Gnomad4 SAS AF: 0.438

Gnomad4 FIN AF: 0.641

Gnomad4 NFE AF: 0.522

Gnomad4 OTH AF: 0.591

Alfa AF: 0.527 Hom.: 41855

Bravo AF: 0.599

Asia WGS AF: 0.613 AC: 2130 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	3.0
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2514299; hg19: chr11-91287525;