rs9921920

Variant names:

• chr16-90049210-C-G
• rs9921920

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 0.614 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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.418 AC: 17327 AN: 41472

American (AMR) AF: 0.587 AC: 8971 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.755 AC: 2617 AN: 3468

East Asian (EAS) AF: 0.359 AC: 1858 AN: 5178

South Asian (SAS) AF: 0.612 AC: 2949 AN: 4816

European-Finnish (FIN) AF: 0.581 AC: 6129 AN: 10556

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.751 AC: 51055 AN: 68012

Other (OTH) AF: 0.660 AC: 1389 AN: 2104

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.31
DANN	Benign	0.67
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs9921920; hg19: chr16-90115618;