rs16909859

Variant names:

• chr9-95442510-G-A
• rs16909859

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 0.14 in 152,192 control chromosomes in the GnomAD database, including 2,229 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 (2229 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.376

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.283 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: 0.140 AC: 21282 AN: 152074 Hom.: 2223 Cov.: 33

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.0330

Gnomad AMR AF: 0.0853

Gnomad ASJ AF: 0.0277

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.0799

Gnomad FIN AF: 0.0937

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0805

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.140 AC: 21338 AN: 152192 Hom.: 2229 Cov.: 33 AF XY: 0.138 AC XY: 10276 AN XY: 74424

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.0854

Gnomad4 ASJ AF: 0.0277

Gnomad4 EAS AF: 0.164

Gnomad4 SAS AF: 0.0806

Gnomad4 FIN AF: 0.0937

Gnomad4 NFE AF: 0.0806

Gnomad4 OTH AF: 0.120

Alfa AF: 0.0865 Hom.: 767

Bravo AF: 0.147

Asia WGS AF: 0.156 AC: 544 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.7
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: rs16909859; hg19: chr9-98204792;