rs1571093

chr9-118784709-T-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;