rs741713

Positions:

• chr14-22303362-C-A

Variant summary

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

The ENST00000656379.1(TRD-AS1):​n.270+97682G>T 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 0.643 in 150,462 control chromosomes in the GnomAD database, including 34,294 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 0.64 (34294 hom., cov: 24)
• Consequence: TRD-AS1 ENST00000656379.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.542

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 (Cadd=0.411).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.847 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+97682G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.643 AC: 96746 AN: 150344 Hom.: 34291 Cov.: 24

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.868

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.810

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.643 AC: 96763 AN: 150462 Hom.: 34294 Cov.: 24 AF XY: 0.652 AC XY: 47884 AN XY: 73448

Gnomad4 AFR AF: 0.318

Gnomad4 AMR AF: 0.760

Gnomad4 ASJ AF: 0.679

Gnomad4 EAS AF: 0.869

Gnomad4 SAS AF: 0.778

Gnomad4 FIN AF: 0.810

Gnomad4 NFE AF: 0.759

Gnomad4 OTH AF: 0.670

Alfa AF: 0.732 Hom.: 48586

Bravo AF: 0.623

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs741713; hg19: -;