16-27381305-G-A

Variant names:

• chr16-27381305-G-A
• rs2382722

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 0.666 in 152,018 control chromosomes in the GnomAD database, including 35,262 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 0.67 (35262 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.69
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.665 AC: 101062 AN: 151900 Hom.: 35203 Cov.: 31

Gnomad AFR AF: 0.889

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.554

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.666 AC: 101183 AN: 152018 Hom.: 35262 Cov.: 31 AF XY: 0.672 AC XY: 49884 AN XY: 74282

African (AFR) AF: 0.889 AC: 36886 AN: 41476

American (AMR) AF: 0.636 AC: 9720 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.460 AC: 1595 AN: 3470

East Asian (EAS) AF: 0.652 AC: 3372 AN: 5170

South Asian (SAS) AF: 0.647 AC: 3112 AN: 4812

European-Finnish (FIN) AF: 0.638 AC: 6735 AN: 10552

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.555 AC: 37678 AN: 67946

Other (OTH) AF: 0.613 AC: 1296 AN: 2114

Alfa AF: 0.534 Hom.: 7642

Bravo AF: 0.671

Asia WGS AF: 0.654 AC: 2274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.0070
DANN	Benign	0.49
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs2382722; hg19: chr16-27392626;