chr11-55909278-C-T

Position:

• chr11-55909278-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 0.162 in 152,116 control chromosomes in the GnomAD database, including 2,516 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 0.16 (2516 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.273 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: 0.162 AC: 24684 AN: 151998 Hom.: 2514 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0217

Gnomad FIN AF: 0.0992

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.162 AC: 24704 AN: 152116 Hom.: 2516 Cov.: 32 AF XY: 0.157 AC XY: 11645 AN XY: 74364

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.0219

Gnomad4 FIN AF: 0.0992

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.165

Alfa AF: 0.159 Hom.: 271

Bravo AF: 0.171

Asia WGS AF: 0.0270 AC: 96 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.77
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7950741; hg19: chr11-55676754;