rs6922617

Variant names:

• chr6-41368363-G-A
• rs6922617

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 0.0611 in 152,226 control chromosomes in the GnomAD database, including 402 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 0.061 (402 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.614

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 (EAS) allele frequency at 95% confidence interval = 0.232 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: 0.0611 AC: 9290 AN: 152108 Hom.: 398 Cov.: 32

Gnomad AFR AF: 0.0295

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0719

Gnomad ASJ AF: 0.0784

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.0938

Gnomad FIN AF: 0.0467

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0637

Gnomad OTH AF: 0.0675

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

GnomAD4 genome AF: 0.0611 AC: 9298 AN: 152226 Hom.: 402 Cov.: 32 AF XY: 0.0621 AC XY: 4620 AN XY: 74406

Gnomad4 AFR AF: 0.0295

Gnomad4 AMR AF: 0.0716

Gnomad4 ASJ AF: 0.0784

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.0934

Gnomad4 FIN AF: 0.0467

Gnomad4 NFE AF: 0.0637

Gnomad4 OTH AF: 0.0735

Alfa AF: 0.0638 Hom.: 490

Bravo AF: 0.0625

Asia WGS AF: 0.181 AC: 632 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	1.1
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6922617; hg19: chr6-41336101;