rs11223548

Positions:

• chr11-133661760-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 0.0442 in 152,230 control chromosomes in the GnomAD database, including 480 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 0.044 (480 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0760

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 (EAS) allele frequency at 95% confidence interval = 0.297 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: 0.0441 AC: 6714 AN: 152112 Hom.: 481 Cov.: 32

Gnomad AFR AF: 0.0696

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0954

Gnomad ASJ AF: 0.0112

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.0488

Gnomad FIN AF: 0.00613

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00516

Gnomad OTH AF: 0.0397

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

GnomAD4 genome AF: 0.0442 AC: 6722 AN: 152230 Hom.: 480 Cov.: 32 AF XY: 0.0465 AC XY: 3461 AN XY: 74420

Gnomad4 AFR AF: 0.0696

Gnomad4 AMR AF: 0.0956

Gnomad4 ASJ AF: 0.0112

Gnomad4 EAS AF: 0.309

Gnomad4 SAS AF: 0.0484

Gnomad4 FIN AF: 0.00613

Gnomad4 NFE AF: 0.00516

Gnomad4 OTH AF: 0.0393

Alfa AF: 0.0185 Hom.: 140

Bravo AF: 0.0538

Asia WGS AF: 0.141 AC: 489 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	0.35
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11223548; hg19: chr11-133531655;