rs534632

Positions:

• chr9-22458981-G-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 0.0613 in 152,114 control chromosomes in the GnomAD database, including 783 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 0.061 (783 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.463

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.186 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: 0.0613 AC: 9324 AN: 151996 Hom.: 786 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0311

Gnomad ASJ AF: 0.0233

Gnomad EAS AF: 0.0399

Gnomad SAS AF: 0.0525

Gnomad FIN AF: 0.000189

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.00447

Gnomad OTH AF: 0.0588

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

GnomAD4 genome AF: 0.0613 AC: 9331 AN: 152114 Hom.: 783 Cov.: 32 AF XY: 0.0596 AC XY: 4430 AN XY: 74362

Gnomad4 AFR AF: 0.189

Gnomad4 AMR AF: 0.0311

Gnomad4 ASJ AF: 0.0233

Gnomad4 EAS AF: 0.0398

Gnomad4 SAS AF: 0.0521

Gnomad4 FIN AF: 0.000189

Gnomad4 NFE AF: 0.00449

Gnomad4 OTH AF: 0.0601

Alfa AF: 0.0304 Hom.: 69

Bravo AF: 0.0690

Asia WGS AF: 0.0660 AC: 230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.3
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs534632; hg19: chr9-22458980;