rs1571093

Variant names:

• chr9-118784709-T-A
• rs1571093

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 0.432 in 152,152 control chromosomes in the GnomAD database, including 16,336 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 0.43 (16336 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.716

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.561 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: 0.433 AC: 65771 AN: 152034 Hom.: 16342 Cov.: 33

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.692

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.470

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

GnomAD4 genome AF: 0.432 AC: 65754 AN: 152152 Hom.: 16336 Cov.: 33 AF XY: 0.427 AC XY: 31752 AN XY: 74370

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.523

Gnomad4 ASJ AF: 0.505

Gnomad4 EAS AF: 0.240

Gnomad4 SAS AF: 0.314

Gnomad4 FIN AF: 0.479

Gnomad4 NFE AF: 0.565

Gnomad4 OTH AF: 0.467

Alfa AF: 0.494 Hom.: 2488

Bravo AF: 0.432

Asia WGS AF: 0.258 AC: 900 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.7
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1571093; hg19: chr9-121546987;