rs1467891

Positions:

• chr14-22304778-T-C

Variant summary

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

The ENST00000656379.1(TRD-AS1):​n.270+96266A>G 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 0.314 in 151,182 control chromosomes in the GnomAD database, including 8,662 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 0.31 (8662 hom., cov: 27)
• Consequence: TRD-AS1 ENST00000656379.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.428

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=-0.57).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.613 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+96266A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47506 AN: 151064 Hom.: 8653 Cov.: 27

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.314 AC: 47531 AN: 151182 Hom.: 8662 Cov.: 27 AF XY: 0.326 AC XY: 24088 AN XY: 73860

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.459

Gnomad4 ASJ AF: 0.292

Gnomad4 EAS AF: 0.631

Gnomad4 SAS AF: 0.443

Gnomad4 FIN AF: 0.423

Gnomad4 NFE AF: 0.339

Gnomad4 OTH AF: 0.319

Alfa AF: 0.340 Hom.: 5865

Bravo AF: 0.311

Asia WGS AF: 0.523 AC: 1814 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	5.5
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1467891; hg19: chr14-22772663;