rs11020124

Variant names:

• chr11-92957495-T-C
• rs11020124

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 0.318 in 151,922 control chromosomes in the GnomAD database, including 7,840 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 0.32 (7840 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.431 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: 0.318 AC: 48245 AN: 151804 Hom.: 7839 Cov.: 31

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.318 AC: 48273 AN: 151922 Hom.: 7840 Cov.: 31 AF XY: 0.320 AC XY: 23756 AN XY: 74236

Gnomad4 AFR AF: 0.359

Gnomad4 AMR AF: 0.234

Gnomad4 ASJ AF: 0.277

Gnomad4 EAS AF: 0.446

Gnomad4 SAS AF: 0.387

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.303

Alfa AF: 0.306 Hom.: 1582

Bravo AF: 0.309

Asia WGS AF: 0.352 AC: 1224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.92
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: rs11020124; hg19: chr11-92690661;