rs16910869

Variant names:

• chr8-139535001-A-G
• rs16910869

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 0.138 in 152,074 control chromosomes in the GnomAD database, including 1,624 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 0.14 (1624 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.706
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.267 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: 0.138 AC: 20961 AN: 151956 Hom.: 1622 Cov.: 31

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.0826

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.138 AC: 20978 AN: 152074 Hom.: 1624 Cov.: 31 AF XY: 0.142 AC XY: 10549 AN XY: 74346

African (AFR) AF: 0.151 AC: 6260 AN: 41488

American (AMR) AF: 0.151 AC: 2305 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 415 AN: 3470

East Asian (EAS) AF: 0.279 AC: 1442 AN: 5170

South Asian (SAS) AF: 0.131 AC: 630 AN: 4806

European-Finnish (FIN) AF: 0.176 AC: 1863 AN: 10578

Middle Eastern (MID) AF: 0.205 AC: 60 AN: 292

European-Non Finnish (NFE) AF: 0.112 AC: 7643 AN: 67986

Other (OTH) AF: 0.135 AC: 285 AN: 2108

Alfa AF: 0.128 Hom.: 161

Bravo AF: 0.138

Asia WGS AF: 0.191 AC: 664 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.5
DANN	Benign	0.80
PhyloP100		0.71

Splicing

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

Other links and lift over

dbSNP: rs16910869; hg19: chr8-140547244;