rs16927158

Variant names:

• chr9-8138580-A-G
• rs16927158

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 0.114 in 151,918 control chromosomes in the GnomAD database, including 1,145 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 0.11 (1145 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.266
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17300 AN: 151802 Hom.: 1142 Cov.: 32

Gnomad AFR AF: 0.0897

Gnomad AMI AF: 0.142

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.0619

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.114 AC: 17314 AN: 151918 Hom.: 1145 Cov.: 32 AF XY: 0.113 AC XY: 8411 AN XY: 74260

African (AFR) AF: 0.0897 AC: 3717 AN: 41438

American (AMR) AF: 0.165 AC: 2517 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 612 AN: 3472

East Asian (EAS) AF: 0.131 AC: 676 AN: 5150

South Asian (SAS) AF: 0.145 AC: 698 AN: 4812

European-Finnish (FIN) AF: 0.0619 AC: 652 AN: 10538

Middle Eastern (MID) AF: 0.123 AC: 36 AN: 292

European-Non Finnish (NFE) AF: 0.118 AC: 7996 AN: 67954

Other (OTH) AF: 0.133 AC: 281 AN: 2106

Alfa AF: 0.124 Hom.: 1897

Bravo AF: 0.121

Asia WGS AF: 0.154 AC: 536 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.85
DANN	Benign	0.31
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs16927158; hg19: chr9-8138580;