rs16903109

Variant names:

• chr8-128565383-T-A
• rs16903109

Your query was ambiguous. Multiple possible variants found:

• chr8-128565383-T-A
• chr8-128565383-T-G

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 0.267 in 152,102 control chromosomes in the GnomAD database, including 7,769 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 0.27 (7769 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.784

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.538 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: 0.266 AC: 40474 AN: 151984 Hom.: 7737 Cov.: 32

Gnomad AFR AF: 0.543

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.0471

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.267 AC: 40560 AN: 152102 Hom.: 7769 Cov.: 32 AF XY: 0.260 AC XY: 19296 AN XY: 74354

Gnomad4 AFR AF: 0.544

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.0466

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.261

Alfa AF: 0.210 Hom.: 601

Bravo AF: 0.283

Asia WGS AF: 0.155 AC: 540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.87
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16903109; hg19: chr8-129577629;