rs9921920

Variant names:

• chr16-90049210-C-G
• rs9921920

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 0.614 in 152,096 control chromosomes in the GnomAD database, including 30,313 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 0.61 (30313 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.745 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: 0.614 AC: 93308 AN: 151978 Hom.: 30311 Cov.: 33

Gnomad AFR AF: 0.418

Gnomad AMI AF: 0.870

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.755

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.751

Gnomad OTH AF: 0.658

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

GnomAD4 genome AF: 0.614 AC: 93329 AN: 152096 Hom.: 30313 Cov.: 33 AF XY: 0.604 AC XY: 44901 AN XY: 74334

Gnomad4 AFR AF: 0.418

Gnomad4 AMR AF: 0.587

Gnomad4 ASJ AF: 0.755

Gnomad4 EAS AF: 0.359

Gnomad4 SAS AF: 0.612

Gnomad4 FIN AF: 0.581

Gnomad4 NFE AF: 0.751

Gnomad4 OTH AF: 0.660

Alfa AF: 0.676 Hom.: 4503

Bravo AF: 0.604

Asia WGS AF: 0.502 AC: 1742 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.31
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9921920; hg19: chr16-90115618;