rs11020442

chr11-93599319-C-A

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 0.19 in 152,130 control chromosomes in the GnomAD database, including 4,066 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 0.19 (4066 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.396 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: 0.190 AC: 28935 AN: 152012 Hom.: 4055 Cov.: 33

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.0724

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.190 AC: 28980 AN: 152130 Hom.: 4066 Cov.: 33 AF XY: 0.185 AC XY: 13787 AN XY: 74380

Gnomad4 AFR AF: 0.401

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.154

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.0724

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.185

Alfa AF: 0.124 Hom.: 1894

Bravo AF: 0.207

Asia WGS AF: 0.138 AC: 481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.8
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11020442; hg19: chr11-93332485;