rs283566

Variant names:

• chr6-51091008-C-G
• rs283566

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 0.56 in 151,976 control chromosomes in the GnomAD database, including 24,460 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 0.56 (24460 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.385

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 = 0.759 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: 0.560 AC: 84968 AN: 151858 Hom.: 24425 Cov.: 31

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.635

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.779

Gnomad SAS AF: 0.550

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.560 AC: 85064 AN: 151976 Hom.: 24460 Cov.: 31 AF XY: 0.567 AC XY: 42073 AN XY: 74246

Gnomad4 AFR AF: 0.673

Gnomad4 AMR AF: 0.484

Gnomad4 ASJ AF: 0.552

Gnomad4 EAS AF: 0.779

Gnomad4 SAS AF: 0.550

Gnomad4 FIN AF: 0.601

Gnomad4 NFE AF: 0.485

Gnomad4 OTH AF: 0.550

Alfa AF: 0.509 Hom.: 11235

Bravo AF: 0.559

Asia WGS AF: 0.636 AC: 2207 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	3.7
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs283566; hg19: chr6-51058721;