rs16910869

Variant names:

• chr8-139535001-A-G
• rs16910869

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.138 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

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.279

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.176

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.135

Alfa AF: 0.128 Hom.: 151

Bravo AF: 0.138

Asia WGS AF: 0.191 AC: 664 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16910869; hg19: chr8-140547244;