rs16929097

Variant names:

• chr9-12521826-G-A
• rs16929097

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 0.045 in 151,672 control chromosomes in the GnomAD database, including 309 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 0.045 (309 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0650
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.112 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: 0.0448 AC: 6789 AN: 151554 Hom.: 303 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0246

Gnomad ASJ AF: 0.0382

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0122

Gnomad FIN AF: 0.00312

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0202

Gnomad OTH AF: 0.0388

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

GnomAD4 genome AF: 0.0450 AC: 6823 AN: 151672 Hom.: 309 Cov.: 32 AF XY: 0.0428 AC XY: 3174 AN XY: 74136

African (AFR) AF: 0.115 AC: 4760 AN: 41396

American (AMR) AF: 0.0245 AC: 371 AN: 15152

Ashkenazi Jewish (ASJ) AF: 0.0382 AC: 132 AN: 3458

East Asian (EAS) AF: 0.00155 AC: 8 AN: 5174

South Asian (SAS) AF: 0.0118 AC: 57 AN: 4820

European-Finnish (FIN) AF: 0.00312 AC: 33 AN: 10582

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0202 AC: 1368 AN: 67774

Other (OTH) AF: 0.0384 AC: 81 AN: 2110

Alfa AF: 0.0300 Hom.: 287

Bravo AF: 0.0500

Asia WGS AF: 0.0190 AC: 66 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.81
DANN	Benign	0.66
PhyloP100		0.065

Splicing

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

Other links and lift over

dbSNP: rs16929097; hg19: chr9-12521826;