16-84261750-A-G

Variant names:

• chr16-84261750-A-G
• rs439927

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 0.936 in 152,034 control chromosomes in the GnomAD database, including 66,907 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 0.94 (66907 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.14
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.09).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.984 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: 0.936 AC: 142218 AN: 151916 Hom.: 66867 Cov.: 30

Gnomad AFR AF: 0.860

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.912

Gnomad ASJ AF: 0.985

Gnomad EAS AF: 0.815

Gnomad SAS AF: 0.909

Gnomad FIN AF: 0.972

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.990

Gnomad OTH AF: 0.944

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

GnomAD4 genome AF: 0.936 AC: 142310 AN: 152034 Hom.: 66907 Cov.: 30 AF XY: 0.934 AC XY: 69435 AN XY: 74316

African (AFR) AF: 0.860 AC: 35634 AN: 41432

American (AMR) AF: 0.911 AC: 13932 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.985 AC: 3413 AN: 3466

East Asian (EAS) AF: 0.815 AC: 4205 AN: 5158

South Asian (SAS) AF: 0.909 AC: 4376 AN: 4814

European-Finnish (FIN) AF: 0.972 AC: 10297 AN: 10590

Middle Eastern (MID) AF: 0.969 AC: 285 AN: 294

European-Non Finnish (NFE) AF: 0.990 AC: 67281 AN: 67972

Other (OTH) AF: 0.937 AC: 1979 AN: 2112

Alfa AF: 0.973 Hom.: 3215

Bravo AF: 0.927

Asia WGS AF: 0.824 AC: 2864 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.093
DANN	Benign	0.084
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs439927; hg19: chr16-84295356;