rs16909981

chr9-95550750-G-C

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/exons	MANE	UniProt

Ensembl

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