rs583973

Variant names:

• chr9-105655931-C-A
• rs583973

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 0.326 in 152,008 control chromosomes in the GnomAD database, including 9,554 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 0.33 (9554 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.380

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.448 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: 0.326 AC: 49556 AN: 151890 Hom.: 9558 Cov.: 32

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.0354

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.326 AC: 49550 AN: 152008 Hom.: 9554 Cov.: 32 AF XY: 0.316 AC XY: 23444 AN XY: 74302

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.333

Gnomad4 ASJ AF: 0.417

Gnomad4 EAS AF: 0.0355

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.338

Gnomad4 NFE AF: 0.452

Gnomad4 OTH AF: 0.340

Alfa AF: 0.421 Hom.: 18717

Bravo AF: 0.322

Asia WGS AF: 0.110 AC: 388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.88
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs583973; hg19: chr9-108418212;