rs588565

Variant names:

• chr6-52928056-C-T
• rs588565

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 0.187 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.187 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

Gnomad4 AFR AF: 0.0576

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.331

Gnomad4 EAS AF: 0.0845

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.259

Gnomad4 OTH AF: 0.217

Alfa AF: 0.251 Hom.: 6870

Bravo AF: 0.180

Asia WGS AF: 0.102 AC: 356 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	1.1
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs588565; hg19: chr6-52792854;