rs17198328

Variant names:

• chr14-22295178-G-A
• rs17198328

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 0.239 in 150,912 control chromosomes in the GnomAD database, including 4,494 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 0.24 (4494 hom., cov: 26)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.81
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRA		n.22295178G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRD-AS1	ENST00000656379.1	n.271-93796C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36002 AN: 150794 Hom.: 4490 Cov.: 26

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.0962

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.239 AC: 36019 AN: 150912 Hom.: 4494 Cov.: 26 AF XY: 0.234 AC XY: 17270 AN XY: 73730

African (AFR) AF: 0.239 AC: 9797 AN: 40962

American (AMR) AF: 0.183 AC: 2755 AN: 15070

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 786 AN: 3458

East Asian (EAS) AF: 0.0962 AC: 495 AN: 5146

South Asian (SAS) AF: 0.187 AC: 898 AN: 4794

European-Finnish (FIN) AF: 0.249 AC: 2599 AN: 10446

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.265 AC: 17979 AN: 67730

Other (OTH) AF: 0.240 AC: 506 AN: 2104

Alfa AF: 0.252 Hom.: 8336

Bravo AF: 0.231

Asia WGS AF: 0.135 AC: 473 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.4
DANN	Benign	0.50
PhyloP100		2.8

Splicing

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

Other links and lift over

dbSNP: rs17198328; hg19: chr14-22763063;