rs588565

Variant names:

• chr6-52928056-C-T
• rs588565

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 0.187 in 152,108 control chromosomes in the GnomAD database, including 3,388 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 0.19 (3388 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 2 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 (NFE) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28389 AN: 151990 Hom.: 3384 Cov.: 32

Gnomad AFR AF: 0.0576

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.0857

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.187 AC: 28387 AN: 152108 Hom.: 3388 Cov.: 32 AF XY: 0.184 AC XY: 13686 AN XY: 74324

African (AFR) AF: 0.0576 AC: 2393 AN: 41516

American (AMR) AF: 0.196 AC: 2996 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 1147 AN: 3466

East Asian (EAS) AF: 0.0845 AC: 438 AN: 5182

South Asian (SAS) AF: 0.150 AC: 721 AN: 4814

European-Finnish (FIN) AF: 0.221 AC: 2330 AN: 10544

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.259 AC: 17639 AN: 67986

Other (OTH) AF: 0.217 AC: 458 AN: 2108

Alfa AF: 0.243 Hom.: 8326

Bravo AF: 0.180

Asia WGS AF: 0.102 AC: 356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.73
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs588565; hg19: chr6-52792854;