rs655763

Positions:

• chr11-109306090-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;