rs17793809

Variant names:

• chr14-22325865-G-A
• rs17793809

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 0.0678 in 151,182 control chromosomes in the GnomAD database, including 426 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 0.068 (426 hom., cov: 25)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0440
• Publications: 4 publications found

Genes affected

TRA (HGNC:12027):

TRD-AS1 (HGNC:56197): (TRD antisense RNA 1)

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 = 0.0869 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRA		n.22325865G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRD-AS1	ENST00000656379.1	n.270+75179C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0678 AC: 10246 AN: 151064 Hom.: 426 Cov.: 25

Gnomad AFR AF: 0.0464

Gnomad AMI AF: 0.165

Gnomad AMR AF: 0.0605

Gnomad ASJ AF: 0.0854

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0623

Gnomad FIN AF: 0.0459

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0888

Gnomad OTH AF: 0.0707

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

GnomAD4 genome AF: 0.0678 AC: 10243 AN: 151182 Hom.: 426 Cov.: 25 AF XY: 0.0663 AC XY: 4893 AN XY: 73854

African (AFR) AF: 0.0463 AC: 1906 AN: 41164

American (AMR) AF: 0.0605 AC: 911 AN: 15060

Ashkenazi Jewish (ASJ) AF: 0.0854 AC: 295 AN: 3456

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5162

South Asian (SAS) AF: 0.0624 AC: 297 AN: 4762

European-Finnish (FIN) AF: 0.0459 AC: 481 AN: 10468

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0888 AC: 6022 AN: 67808

Other (OTH) AF: 0.0690 AC: 145 AN: 2100

Alfa AF: 0.0837 Hom.: 970

Bravo AF: 0.0682

Asia WGS AF: 0.0300 AC: 105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.4
DANN	Benign	0.48
PhyloP100		0.044

Splicing

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

Other links and lift over

dbSNP: rs17793809; hg19: chr14-22794295;