rs1569209

Variant names:

• chr8-19972659-T-G
• rs1569209

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 0.0601 in 152,278 control chromosomes in the GnomAD database, including 357 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 0.060 (357 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.598

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.082 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: 0.0602 AC: 9158 AN: 152160 Hom.: 358 Cov.: 32

Gnomad AFR AF: 0.0168

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.0614

Gnomad ASJ AF: 0.0962

Gnomad EAS AF: 0.0285

Gnomad SAS AF: 0.0659

Gnomad FIN AF: 0.0680

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0838

Gnomad OTH AF: 0.0664

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

GnomAD4 genome AF: 0.0601 AC: 9149 AN: 152278 Hom.: 357 Cov.: 32 AF XY: 0.0592 AC XY: 4405 AN XY: 74450

Gnomad4 AFR AF: 0.0168

Gnomad4 AMR AF: 0.0613

Gnomad4 ASJ AF: 0.0962

Gnomad4 EAS AF: 0.0284

Gnomad4 SAS AF: 0.0655

Gnomad4 FIN AF: 0.0680

Gnomad4 NFE AF: 0.0839

Gnomad4 OTH AF: 0.0658

Alfa AF: 0.0597 Hom.: 63

Bravo AF: 0.0581

Asia WGS AF: 0.0470 AC: 162 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.4
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1569209; hg19: chr8-19830170;