rs11029744

Variant names:

• chr11-26930910-G-T
• rs11029744

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.137 AC: 5672 AN: 41470

American (AMR) AF: 0.0248 AC: 379 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0360 AC: 125 AN: 3468

East Asian (EAS) AF: 0.00387 AC: 20 AN: 5172

South Asian (SAS) AF: 0.0400 AC: 193 AN: 4822

European-Finnish (FIN) AF: 0.0109 AC: 115 AN: 10598

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0209 AC: 1422 AN: 67992

Other (OTH) AF: 0.0502 AC: 106 AN: 2110

Alfa AF: 0.0315 Hom.: 112

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
PhyloP100		0.013

Splicing

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

Other links and lift over

dbSNP: rs11029744; hg19: chr11-26952457;