rs569205

Variant names:

• chr8-27619502-T-A
• rs569205

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 0.672 in 152,180 control chromosomes in the GnomAD database, including 35,385 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 0.67 (35385 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.849 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: 0.672 AC: 102154 AN: 152062 Hom.: 35335 Cov.: 33

Gnomad AFR AF: 0.857

Gnomad AMI AF: 0.609

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.644

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

GnomAD4 genome AF: 0.672 AC: 102263 AN: 152180 Hom.: 35385 Cov.: 33 AF XY: 0.668 AC XY: 49714 AN XY: 74392

Gnomad4 AFR AF: 0.857

Gnomad4 AMR AF: 0.619

Gnomad4 ASJ AF: 0.632

Gnomad4 EAS AF: 0.532

Gnomad4 SAS AF: 0.541

Gnomad4 FIN AF: 0.598

Gnomad4 NFE AF: 0.606

Gnomad4 OTH AF: 0.644

Alfa AF: 0.652 Hom.: 4081

Bravo AF: 0.682

Asia WGS AF: 0.517 AC: 1798 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.3
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs569205; hg19: chr8-27477019;