11-121333892-A-G

Variant names:

• chr11-121333892-A-G
• rs4936613

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 0.887 in 152,214 control chromosomes in the GnomAD database, including 60,042 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 0.89 (60042 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.204

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 (AFR) allele frequency at 95% confidence interval = 0.926 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: 0.887 AC: 134960 AN: 152096 Hom.: 59989 Cov.: 32

Gnomad AFR AF: 0.934

Gnomad AMI AF: 0.952

Gnomad AMR AF: 0.903

Gnomad ASJ AF: 0.899

Gnomad EAS AF: 0.911

Gnomad SAS AF: 0.861

Gnomad FIN AF: 0.844

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.861

Gnomad OTH AF: 0.882

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

GnomAD4 genome AF: 0.887 AC: 135073 AN: 152214 Hom.: 60042 Cov.: 32 AF XY: 0.887 AC XY: 65962 AN XY: 74404

Gnomad4 AFR AF: 0.934

Gnomad4 AMR AF: 0.903

Gnomad4 ASJ AF: 0.899

Gnomad4 EAS AF: 0.911

Gnomad4 SAS AF: 0.861

Gnomad4 FIN AF: 0.844

Gnomad4 NFE AF: 0.861

Gnomad4 OTH AF: 0.880

Alfa AF: 0.881 Hom.: 11164

Bravo AF: 0.896

Asia WGS AF: 0.882 AC: 3067 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	0.30
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4936613; hg19: chr11-121204601;