16-52423230-A-G

Variant names:

• chr16-52423230-A-G
• rs8049226

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 0.507 in 151,908 control chromosomes in the GnomAD database, including 21,592 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 (21592 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.104
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.782 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: 0.507 AC: 76913 AN: 151790 Hom.: 21559 Cov.: 32

Gnomad AFR AF: 0.728

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.803

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.507 AC: 76993 AN: 151908 Hom.: 21592 Cov.: 32 AF XY: 0.512 AC XY: 38016 AN XY: 74210

African (AFR) AF: 0.728 AC: 30192 AN: 41448

American (AMR) AF: 0.484 AC: 7382 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 1285 AN: 3464

East Asian (EAS) AF: 0.802 AC: 4130 AN: 5148

South Asian (SAS) AF: 0.573 AC: 2750 AN: 4800

European-Finnish (FIN) AF: 0.407 AC: 4301 AN: 10556

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.373 AC: 25346 AN: 67914

Other (OTH) AF: 0.490 AC: 1034 AN: 2112

Alfa AF: 0.419 Hom.: 47459

Bravo AF: 0.524

Asia WGS AF: 0.672 AC: 2336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	3.4
DANN	Benign	0.78
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs8049226; hg19: chr16-52457142;