rs9923476

Variant names:

• chr16-86447489-C-G
• rs9923476

Your query was ambiguous. Multiple possible variants found:

• chr16-86447489-C-G
• chr16-86447489-C-T

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 0.542 in 151,996 control chromosomes in the GnomAD database, including 22,992 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 0.54 (22992 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.489
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.612 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: 0.542 AC: 82360 AN: 151878 Hom.: 22985 Cov.: 32

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.436

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.542 AC: 82381 AN: 151996 Hom.: 22992 Cov.: 32 AF XY: 0.542 AC XY: 40274 AN XY: 74308

African (AFR) AF: 0.425 AC: 17598 AN: 41400

American (AMR) AF: 0.496 AC: 7577 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1893 AN: 3470

East Asian (EAS) AF: 0.436 AC: 2253 AN: 5164

South Asian (SAS) AF: 0.422 AC: 2031 AN: 4814

European-Finnish (FIN) AF: 0.682 AC: 7215 AN: 10580

Middle Eastern (MID) AF: 0.531 AC: 155 AN: 292

European-Non Finnish (NFE) AF: 0.617 AC: 41948 AN: 67974

Other (OTH) AF: 0.539 AC: 1140 AN: 2114

Alfa AF: 0.464 Hom.: 1422

Bravo AF: 0.522

Asia WGS AF: 0.425 AC: 1482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.67
DANN	Benign	0.64
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs9923476; hg19: chr16-86481095;