chr9-22488679-G-A

Variant names:

• chr9-22488679-G-A
• rs586716

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 0.575 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.824 AC: 34173 AN: 41458

American (AMR) AF: 0.532 AC: 8098 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.531 AC: 1841 AN: 3468

East Asian (EAS) AF: 0.792 AC: 4070 AN: 5140

South Asian (SAS) AF: 0.557 AC: 2681 AN: 4816

European-Finnish (FIN) AF: 0.548 AC: 5783 AN: 10562

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.426 AC: 28901 AN: 67918

Other (OTH) AF: 0.559 AC: 1180 AN: 2110

Alfa AF: 0.475 Hom.: 31947

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
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs586716; hg19: chr9-22488678;