rs16909285

Variant names:

• chr9-25281392-G-T
• rs16909285

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 0.0617 in 152,114 control chromosomes in the GnomAD database, including 486 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 0.062 (486 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.754
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.137 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: 0.0617 AC: 9383 AN: 151996 Hom.: 487 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0893

Gnomad ASJ AF: 0.0130

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.0327

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0178

Gnomad OTH AF: 0.0526

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

GnomAD4 genome AF: 0.0617 AC: 9388 AN: 152114 Hom.: 486 Cov.: 32 AF XY: 0.0645 AC XY: 4798 AN XY: 74370

African (AFR) AF: 0.120 AC: 4991 AN: 41486

American (AMR) AF: 0.0889 AC: 1357 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0130 AC: 45 AN: 3470

East Asian (EAS) AF: 0.118 AC: 609 AN: 5166

South Asian (SAS) AF: 0.146 AC: 702 AN: 4824

European-Finnish (FIN) AF: 0.0327 AC: 347 AN: 10610

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0178 AC: 1210 AN: 67976

Other (OTH) AF: 0.0549 AC: 116 AN: 2114

Alfa AF: 0.0480 Hom.: 163

Bravo AF: 0.0679

Asia WGS AF: 0.137 AC: 473 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.40
DANN	Benign	0.78
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs16909285; hg19: chr9-25281390;