rs16917898

Variant names:

• chr9-32116522-G-A
• rs16917898

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 0.105 in 152,050 control chromosomes in the GnomAD database, including 943 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 0.11 (943 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.508
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.211 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: 0.105 AC: 15992 AN: 151932 Hom.: 944 Cov.: 32

Gnomad AFR AF: 0.0847

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.0892

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.0701

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.105 AC: 15998 AN: 152050 Hom.: 943 Cov.: 32 AF XY: 0.105 AC XY: 7788 AN XY: 74332

African (AFR) AF: 0.0847 AC: 3515 AN: 41496

American (AMR) AF: 0.0892 AC: 1361 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 512 AN: 3468

East Asian (EAS) AF: 0.170 AC: 871 AN: 5124

South Asian (SAS) AF: 0.222 AC: 1067 AN: 4812

European-Finnish (FIN) AF: 0.0701 AC: 742 AN: 10588

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7495 AN: 67976

Other (OTH) AF: 0.123 AC: 260 AN: 2114

Alfa AF: 0.108 Hom.: 1309

Bravo AF: 0.103

Asia WGS AF: 0.234 AC: 815 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.061
DANN	Benign	0.71
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs16917898; hg19: chr9-32116520;