16-84200540-G-A

Variant names:

• chr16-84200540-G-A
• rs8045919

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 0.37 in 151,866 control chromosomes in the GnomAD database, including 11,600 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 0.37 (11600 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.228
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.369 AC: 56066 AN: 151748 Hom.: 11571 Cov.: 32

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.370 AC: 56134 AN: 151866 Hom.: 11600 Cov.: 32 AF XY: 0.367 AC XY: 27205 AN XY: 74222

African (AFR) AF: 0.553 AC: 22890 AN: 41388

American (AMR) AF: 0.262 AC: 3993 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 880 AN: 3470

East Asian (EAS) AF: 0.465 AC: 2386 AN: 5130

South Asian (SAS) AF: 0.226 AC: 1089 AN: 4810

European-Finnish (FIN) AF: 0.346 AC: 3651 AN: 10556

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20121 AN: 67950

Other (OTH) AF: 0.369 AC: 778 AN: 2110

Alfa AF: 0.317 Hom.: 30913

Bravo AF: 0.373

Asia WGS AF: 0.333 AC: 1162 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.92
DANN	Benign	0.45
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs8045919; hg19: chr16-84234146;