rs1569209

Positions:

• chr8-19972659-T-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;