rs533393

Variant names:

• chr6-80939927-A-G
• rs533393

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 0.514 in 151,974 control chromosomes in the GnomAD database, including 20,766 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 0.51 (20766 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.931
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.683 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: 0.514 AC: 78031 AN: 151856 Hom.: 20710 Cov.: 32

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.702

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.442

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.514 AC: 78140 AN: 151974 Hom.: 20766 Cov.: 32 AF XY: 0.519 AC XY: 38539 AN XY: 74282

African (AFR) AF: 0.641 AC: 26553 AN: 41444

American (AMR) AF: 0.480 AC: 7311 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.481 AC: 1667 AN: 3468

East Asian (EAS) AF: 0.702 AC: 3622 AN: 5156

South Asian (SAS) AF: 0.608 AC: 2933 AN: 4826

European-Finnish (FIN) AF: 0.458 AC: 4840 AN: 10568

Middle Eastern (MID) AF: 0.438 AC: 127 AN: 290

European-Non Finnish (NFE) AF: 0.436 AC: 29612 AN: 67952

Other (OTH) AF: 0.506 AC: 1068 AN: 2112

Alfa AF: 0.464 Hom.: 9304

Bravo AF: 0.519

Asia WGS AF: 0.666 AC: 2316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.15
DANN	Benign	0.22
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs533393; hg19: chr6-81649644;