rs4982599

Positions:

• chr14-22279581-G-A

Variant summary

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

The ENST00000656379.1(TRD-AS1):​n.271-78199C>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 0.325 in 150,012 control chromosomes in the GnomAD database, including 8,922 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 (8922 hom., cov: 25)
• Consequence: TRD-AS1 ENST00000656379.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.290

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.492 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRD-AS1	ENST00000656379.1	n.271-78199C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.325 AC: 48661 AN: 149894 Hom.: 8886 Cov.: 25

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.325 AC: 48761 AN: 150012 Hom.: 8922 Cov.: 25 AF XY: 0.323 AC XY: 23619 AN XY: 73172

Gnomad4 AFR AF: 0.498

Gnomad4 AMR AF: 0.262

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.458

Gnomad4 SAS AF: 0.353

Gnomad4 FIN AF: 0.212

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.323

Alfa AF: 0.280 Hom.: 2953

Bravo AF: 0.337

Asia WGS AF: 0.418 AC: 1454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.0
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4982599; hg19: chr14-22747464;