rs283566

Variant names:

• chr6-51091008-C-G
• rs283566

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.673 AC: 27908 AN: 41484

American (AMR) AF: 0.484 AC: 7387 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1913 AN: 3466

East Asian (EAS) AF: 0.779 AC: 4032 AN: 5174

South Asian (SAS) AF: 0.550 AC: 2650 AN: 4816

European-Finnish (FIN) AF: 0.601 AC: 6347 AN: 10554

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.485 AC: 32947 AN: 67904

Other (OTH) AF: 0.550 AC: 1161 AN: 2112

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
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs283566; hg19: chr6-51058721;