rs11042594

chr11-2096173-A-G

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 0.759 in 151,498 control chromosomes in the GnomAD database, including 44,457 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 0.76 (44457 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.552

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.899 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: 0.758 AC: 114811 AN: 151384 Hom.: 44383 Cov.: 28

Gnomad AFR AF: 0.907

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.774

Gnomad ASJ AF: 0.669

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.734

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.730

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

GnomAD4 genome AF: 0.759 AC: 114943 AN: 151498 Hom.: 44457 Cov.: 28 AF XY: 0.754 AC XY: 55741 AN XY: 73960

Gnomad4 AFR AF: 0.907

Gnomad4 AMR AF: 0.774

Gnomad4 ASJ AF: 0.669

Gnomad4 EAS AF: 0.503

Gnomad4 SAS AF: 0.545

Gnomad4 FIN AF: 0.734

Gnomad4 NFE AF: 0.709

Gnomad4 OTH AF: 0.730

Alfa AF: 0.712 Hom.: 50636

Bravo AF: 0.772

Asia WGS AF: 0.568 AC: 1977 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
Cadd	Benign	0.54
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11042594; hg19: chr11-2117403;