rs16909859

Positions:

• chr9-95442510-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;