chr14-22295178-G-A

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656379.1. You can select a different transcript below to see updated ACMG assignments.

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
	TRD-AS1	ENST00000656379.1		n.271-93796C>T		intron	N/A

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 v4.9

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;