16-2274302-A-G

Variant names:

• chr16-2274302-A-G
• rs161427

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 0.511 in 152,110 control chromosomes in the GnomAD database, including 21,030 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 0.51 (21030 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.181
• 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 (NFE) allele frequency at 95% confidence interval = 0.591 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: 0.511 AC: 77721 AN: 151992 Hom.: 21000 Cov.: 33

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.608

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.511 AC: 77799 AN: 152110 Hom.: 21030 Cov.: 33 AF XY: 0.513 AC XY: 38162 AN XY: 74344

African (AFR) AF: 0.322 AC: 13349 AN: 41518

American (AMR) AF: 0.594 AC: 9073 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.543 AC: 1881 AN: 3466

East Asian (EAS) AF: 0.488 AC: 2515 AN: 5156

South Asian (SAS) AF: 0.487 AC: 2349 AN: 4828

European-Finnish (FIN) AF: 0.608 AC: 6431 AN: 10582

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.595 AC: 40468 AN: 67964

Other (OTH) AF: 0.542 AC: 1145 AN: 2112

Alfa AF: 0.575 Hom.: 44314

Bravo AF: 0.507

Asia WGS AF: 0.466 AC: 1620 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	2.0
DANN	Benign	0.34
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs161427; hg19: chr16-2324303;