rs16909981

Variant names:

• chr9-95550750-G-C
• rs16909981

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 0.194 in 152,198 control chromosomes in the GnomAD database, including 3,990 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 0.19 (3990 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.58

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.374 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: 0.194 AC: 29517 AN: 152080 Hom.: 3958 Cov.: 33

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.0888

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.0951

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.194 AC: 29598 AN: 152198 Hom.: 3990 Cov.: 33 AF XY: 0.191 AC XY: 14192 AN XY: 74420

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.0888

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.0949

Gnomad4 FIN AF: 0.121

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.178

Alfa AF: 0.180 Hom.: 381

Bravo AF: 0.203

Asia WGS AF: 0.165 AC: 571 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.028
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: rs16909981; hg19: chr9-98313032;