rs11845134

chr14-22313945-C-T

Variant summary

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

The ENST00000656379.1(TRD-AS1):n.270+87099G>A 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 0.334 in 150,760 control chromosomes in the GnomAD database, including 12,509 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 0.33 (12509 hom., cov: 26)
• Consequence: TRD-AS1 ENST00000656379.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.701 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.270+87099G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50248 AN: 150642 Hom.: 12467 Cov.: 26

Gnomad AFR AF: 0.707

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.334 AC: 50344 AN: 150760 Hom.: 12509 Cov.: 26 AF XY: 0.334 AC XY: 24560 AN XY: 73620

Gnomad4 AFR AF: 0.707

Gnomad4 AMR AF: 0.229

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.314

Alfa AF: 0.201 Hom.: 7566

Bravo AF: 0.350

Asia WGS AF: 0.267 AC: 926 AN: 3476

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
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11845134; hg19: chr14-22782377;