chr14-22020269-G-A

Variant names:

• chr14-22020269-G-A
• rs979027

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 0.46 in 151,052 control chromosomes in the GnomAD database, including 17,251 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 0.46 (17251 hom., cov: 26)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 4 publications found

Genes affected

TRA (HGNC:12027):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.629 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: 0.460 AC: 69467 AN: 150934 Hom.: 17210 Cov.: 26

Gnomad AFR AF: 0.635

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.460 AC: 69553 AN: 151052 Hom.: 17251 Cov.: 26 AF XY: 0.456 AC XY: 33677 AN XY: 73784

African (AFR) AF: 0.635 AC: 26096 AN: 41098

American (AMR) AF: 0.530 AC: 8005 AN: 15114

Ashkenazi Jewish (ASJ) AF: 0.449 AC: 1553 AN: 3458

East Asian (EAS) AF: 0.443 AC: 2272 AN: 5124

South Asian (SAS) AF: 0.472 AC: 2230 AN: 4728

European-Finnish (FIN) AF: 0.279 AC: 2928 AN: 10482

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.370 AC: 25058 AN: 67750

Other (OTH) AF: 0.447 AC: 938 AN: 2098

Alfa AF: 0.406 Hom.: 10673

Bravo AF: 0.484

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs979027; hg19: chr14-22488509;