14-28689334-G-A

Variant names:

• chr14-28689334-G-A
• rs176261

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 0.585 in 151,914 control chromosomes in the GnomAD database, including 26,423 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 0.59 (26423 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.249
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.627 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: 0.586 AC: 88911 AN: 151796 Hom.: 26420 Cov.: 32

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.644

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.695

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.585 AC: 88935 AN: 151914 Hom.: 26423 Cov.: 32 AF XY: 0.586 AC XY: 43503 AN XY: 74234

African (AFR) AF: 0.505 AC: 20905 AN: 41420

American (AMR) AF: 0.515 AC: 7849 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.534 AC: 1854 AN: 3472

East Asian (EAS) AF: 0.644 AC: 3330 AN: 5172

South Asian (SAS) AF: 0.535 AC: 2574 AN: 4808

European-Finnish (FIN) AF: 0.695 AC: 7344 AN: 10568

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.632 AC: 42920 AN: 67924

Other (OTH) AF: 0.581 AC: 1222 AN: 2102

Alfa AF: 0.605 Hom.: 5662

Bravo AF: 0.570

Asia WGS AF: 0.594 AC: 2064 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	1.6
DANN	Benign	0.20
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs176261; hg19: chr14-29158540;