11-109306090-C-T

Variant names:

• chr11-109306090-C-T
• rs655763

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 0.585 in 151,934 control chromosomes in the GnomAD database, including 27,145 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 (27145 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0560

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.67 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: 0.586 AC: 88907 AN: 151816 Hom.: 27151 Cov.: 31

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.735

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.676

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.585 AC: 88921 AN: 151934 Hom.: 27145 Cov.: 31 AF XY: 0.585 AC XY: 43436 AN XY: 74254

Gnomad4 AFR AF: 0.422

Gnomad4 AMR AF: 0.534

Gnomad4 ASJ AF: 0.585

Gnomad4 EAS AF: 0.506

Gnomad4 SAS AF: 0.626

Gnomad4 FIN AF: 0.735

Gnomad4 NFE AF: 0.675

Gnomad4 OTH AF: 0.568

Alfa AF: 0.637 Hom.: 30209

Bravo AF: 0.564

Asia WGS AF: 0.555 AC: 1930 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.9
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs655763; hg19: chr11-109176817;