rs11154022

Variant names:

• chr6-121427396-A-G
• rs11154022

Your query was ambiguous. Multiple possible variants found:

• chr6-121427396-A-G
• chr6-121427396-A-T

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 0.712 in 148,404 control chromosomes in the GnomAD database, including 37,510 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 0.71 (37510 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.910

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.811 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: 0.712 AC: 105564 AN: 148288 Hom.: 37477 Cov.: 29

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.731

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.675

Gnomad MID AF: 0.545

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.691

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

GnomAD4 genome AF: 0.712 AC: 105655 AN: 148404 Hom.: 37510 Cov.: 29 AF XY: 0.711 AC XY: 51548 AN XY: 72472

Gnomad4 AFR AF: 0.819

Gnomad4 AMR AF: 0.730

Gnomad4 ASJ AF: 0.561

Gnomad4 EAS AF: 0.516

Gnomad4 SAS AF: 0.605

Gnomad4 FIN AF: 0.675

Gnomad4 NFE AF: 0.682

Gnomad4 OTH AF: 0.689

Alfa AF: 0.679 Hom.: 36658

Bravo AF: 0.745

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.84
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: rs11154022; hg19: chr6-121748542; COSMIC: COSV69423777;