rs569214

Variant names:

• chr8-27630273-G-T
• rs569214

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 0.307 in 151,824 control chromosomes in the GnomAD database, including 8,023 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 0.31 (8023 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.530

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.485 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: 0.307 AC: 46556 AN: 151706 Hom.: 8023 Cov.: 31

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.307 AC: 46564 AN: 151824 Hom.: 8023 Cov.: 31 AF XY: 0.311 AC XY: 23090 AN XY: 74194

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.448

Gnomad4 EAS AF: 0.501

Gnomad4 SAS AF: 0.474

Gnomad4 FIN AF: 0.369

Gnomad4 NFE AF: 0.357

Gnomad4 OTH AF: 0.340

Alfa AF: 0.362 Hom.: 17678

Bravo AF: 0.296

Asia WGS AF: 0.498 AC: 1732 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.7
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs569214; hg19: chr8-27487790; COSMIC: COSV57271879;