rs6084946

Variant names:

• chr20-569274-G-C
• rs6084946

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 0.304 in 152,142 control chromosomes in the GnomAD database, including 7,998 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 0.30 (7998 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.348

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.473 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: 0.304 AC: 46174 AN: 152024 Hom.: 7991 Cov.: 33

Gnomad AFR AF: 0.479

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.304 AC: 46204 AN: 152142 Hom.: 7998 Cov.: 33 AF XY: 0.301 AC XY: 22395 AN XY: 74374

Gnomad4 AFR AF: 0.479

Gnomad4 AMR AF: 0.320

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.220

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.216

Gnomad4 NFE AF: 0.218

Gnomad4 OTH AF: 0.293

Alfa AF: 0.266 Hom.: 796

Bravo AF: 0.321

Asia WGS AF: 0.242 AC: 844 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.0
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6084946; hg19: chr20-549918;