rs17116039

chr14-22284990-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000656379.1(TRD-AS1):n.271-83608T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 151,010 control chromosomes in the GnomAD database, including 5,389 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 0.26 (5389 hom., cov: 26)
• Consequence: TRD-AS1 ENST00000656379.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.225

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRD-AS1	ENST00000656379.1	n.271-83608T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.264 AC: 39855 AN: 150892 Hom.: 5379 Cov.: 26

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.176

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.0913

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.264 AC: 39907 AN: 151010 Hom.: 5389 Cov.: 26 AF XY: 0.261 AC XY: 19266 AN XY: 73774

Gnomad4 AFR AF: 0.243

Gnomad4 AMR AF: 0.260

Gnomad4 ASJ AF: 0.226

Gnomad4 EAS AF: 0.0909

Gnomad4 SAS AF: 0.301

Gnomad4 FIN AF: 0.284

Gnomad4 NFE AF: 0.289

Gnomad4 OTH AF: 0.259

Alfa AF: 0.282 Hom.: 8048

Bravo AF: 0.261

Asia WGS AF: 0.208 AC: 726 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.5
Dann	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17116039; hg19: chr14-22752873;