rs6922466

Variant names:

• chr6-138123793-A-G
• rs6922466

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 0.211 in 152,070 control chromosomes in the GnomAD database, including 3,657 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 0.21 (3657 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.948

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.403 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: 0.211 AC: 32005 AN: 151952 Hom.: 3651 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.211 AC: 32035 AN: 152070 Hom.: 3657 Cov.: 32 AF XY: 0.208 AC XY: 15454 AN XY: 74336

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.262

Gnomad4 EAS AF: 0.181

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.236

Alfa AF: 0.238 Hom.: 5840

Bravo AF: 0.206

Asia WGS AF: 0.318 AC: 1108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.47
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6922466; hg19: chr6-138444930;