rs11042594

Variant names:

• chr11-2096173-A-G
• rs11042594

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;