rs11029744

Positions:

• chr11-26930910-G-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 0.0529 in 152,108 control chromosomes in the GnomAD database, including 432 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 0.053 (432 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0528 AC: 8029 AN: 151992 Hom.: 431 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0249

Gnomad ASJ AF: 0.0360

Gnomad EAS AF: 0.00386

Gnomad SAS AF: 0.0408

Gnomad FIN AF: 0.0109

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0209

Gnomad OTH AF: 0.0508

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

GnomAD4 genome AF: 0.0529 AC: 8045 AN: 152108 Hom.: 432 Cov.: 32 AF XY: 0.0509 AC XY: 3789 AN XY: 74368

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.0248

Gnomad4 ASJ AF: 0.0360

Gnomad4 EAS AF: 0.00387

Gnomad4 SAS AF: 0.0400

Gnomad4 FIN AF: 0.0109

Gnomad4 NFE AF: 0.0209

Gnomad4 OTH AF: 0.0502

Alfa AF: 0.0308 Hom.: 78

Bravo AF: 0.0573

Asia WGS AF: 0.0310 AC: 109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.66
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11029744; hg19: chr11-26952457;