chr6-121427396-A-G

Variant names:

• chr6-121427396-A-G
• rs11154022

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 17 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.819 AC: 32695 AN: 39938

American (AMR) AF: 0.730 AC: 10952 AN: 15000

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1875 AN: 3342

East Asian (EAS) AF: 0.516 AC: 2651 AN: 5136

South Asian (SAS) AF: 0.605 AC: 2860 AN: 4724

European-Finnish (FIN) AF: 0.675 AC: 6932 AN: 10270

Middle Eastern (MID) AF: 0.545 AC: 157 AN: 288

European-Non Finnish (NFE) AF: 0.682 AC: 45550 AN: 66780

Other (OTH) AF: 0.689 AC: 1422 AN: 2064

Alfa AF: 0.684 Hom.: 44421

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
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs11154022; hg19: chr6-121748542; COSMIC: COSV69423777;