14-22020269-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRA		n.22020269G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;