rs7859562

Variant names:

• chr9-1510590-A-G
• rs7859562

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 0.154 in 152,200 control chromosomes in the GnomAD database, including 2,205 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 0.15 (2205 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.435
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23429 AN: 152082 Hom.: 2202 Cov.: 33

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.0671

Gnomad SAS AF: 0.0436

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.154 AC: 23449 AN: 152200 Hom.: 2205 Cov.: 33 AF XY: 0.150 AC XY: 11195 AN XY: 74418

African (AFR) AF: 0.265 AC: 10991 AN: 41480

American (AMR) AF: 0.112 AC: 1718 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 604 AN: 3470

East Asian (EAS) AF: 0.0672 AC: 348 AN: 5176

South Asian (SAS) AF: 0.0439 AC: 212 AN: 4830

European-Finnish (FIN) AF: 0.104 AC: 1105 AN: 10614

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7905 AN: 68020

Other (OTH) AF: 0.153 AC: 324 AN: 2112

Alfa AF: 0.130 Hom.: 349

Bravo AF: 0.161

Asia WGS AF: 0.0660 AC: 233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	6.2
DANN	Benign	0.68
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs7859562; hg19: chr9-1510590;