rs1571093

Variant names:

• chr9-118784709-T-A
• rs1571093

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.192 AC: 7990 AN: 41538

American (AMR) AF: 0.523 AC: 7995 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1752 AN: 3468

East Asian (EAS) AF: 0.240 AC: 1240 AN: 5166

South Asian (SAS) AF: 0.314 AC: 1515 AN: 4822

European-Finnish (FIN) AF: 0.479 AC: 5061 AN: 10560

Middle Eastern (MID) AF: 0.462 AC: 135 AN: 292

European-Non Finnish (NFE) AF: 0.565 AC: 38447 AN: 67994

Other (OTH) AF: 0.467 AC: 988 AN: 2116

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.7
DANN	Benign	0.70
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs1571093; hg19: chr9-121546987;