rs11154022

chr6-121427396-A-Gchr6-121427396-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;