6-166920485-A-G

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 0.697 in 151,452 control chromosomes in the GnomAD database, including 41,375 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 0.70 (41375 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.197

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 = 0.88 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: 0.697 AC: 105478 AN: 151336 Hom.: 41371 Cov.: 32

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.783

Gnomad EAS AF: 0.901

Gnomad SAS AF: 0.816

Gnomad FIN AF: 0.881

Gnomad MID AF: 0.761

Gnomad NFE AF: 0.847

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.697 AC: 105491 AN: 151452 Hom.: 41375 Cov.: 32 AF XY: 0.703 AC XY: 52075 AN XY: 74088

Gnomad4 AFR AF: 0.306

Gnomad4 AMR AF: 0.823

Gnomad4 ASJ AF: 0.783

Gnomad4 EAS AF: 0.901

Gnomad4 SAS AF: 0.816

Gnomad4 FIN AF: 0.881

Gnomad4 NFE AF: 0.847

Gnomad4 OTH AF: 0.733

Alfa AF: 0.816 Hom.: 70752

Bravo AF: 0.676

Asia WGS AF: 0.777 AC: 2702 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	4.3
Dann	Benign	0.59

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs9355606; hg19: chr6-167333973;