rs583973

Positions:

• chr9-105655931-C-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 0.326 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;