16-82612728-A-G

Variant names:

• chr16-82612728-A-G
• rs3844412

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 0.516 in 151,898 control chromosomes in the GnomAD database, including 21,081 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 0.52 (21081 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.729 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: 0.515 AC: 78231 AN: 151780 Hom.: 21047 Cov.: 32

Gnomad AFR AF: 0.656

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.749

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.516 AC: 78309 AN: 151898 Hom.: 21081 Cov.: 32 AF XY: 0.516 AC XY: 38318 AN XY: 74216

African (AFR) AF: 0.657 AC: 27191 AN: 41406

American (AMR) AF: 0.499 AC: 7607 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1296 AN: 3464

East Asian (EAS) AF: 0.749 AC: 3859 AN: 5154

South Asian (SAS) AF: 0.500 AC: 2411 AN: 4824

European-Finnish (FIN) AF: 0.453 AC: 4763 AN: 10522

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.436 AC: 29660 AN: 67958

Other (OTH) AF: 0.492 AC: 1041 AN: 2114

Alfa AF: 0.466 Hom.: 75662

Bravo AF: 0.530

Asia WGS AF: 0.601 AC: 2089 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.26
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs3844412; hg19: chr16-82646333;