rs586716

Positions:

• chr9-22488679-G-A
• chr9-22488679-G-C

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 0.575 in 151,890 control chromosomes in the GnomAD database, including 27,506 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 0.58 (27506 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.582

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.817 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: 0.575 AC: 87247 AN: 151772 Hom.: 27457 Cov.: 32

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.575 AC: 87357 AN: 151890 Hom.: 27506 Cov.: 32 AF XY: 0.580 AC XY: 43054 AN XY: 74216

Gnomad4 AFR AF: 0.824

Gnomad4 AMR AF: 0.532

Gnomad4 ASJ AF: 0.531

Gnomad4 EAS AF: 0.792

Gnomad4 SAS AF: 0.557

Gnomad4 FIN AF: 0.548

Gnomad4 NFE AF: 0.426

Gnomad4 OTH AF: 0.559

Alfa AF: 0.458 Hom.: 18087

Bravo AF: 0.588

Asia WGS AF: 0.689 AC: 2398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.72
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs586716; hg19: chr9-22488678;