rs3811266

Positions:

• chr14-22279172-A-G
• chr14-22279172-A-T

Variant summary

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

The ENST00000656379.1(TRD-AS1):​n.271-77790T>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 0.317 in 151,206 control chromosomes in the GnomAD database, including 8,531 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 0.32 (8531 hom., cov: 27)
• Consequence: TRD-AS1 ENST00000656379.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.535

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.468 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.271-77790T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.317 AC: 47881 AN: 151088 Hom.: 8498 Cov.: 27

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.317 AC: 47974 AN: 151206 Hom.: 8531 Cov.: 27 AF XY: 0.316 AC XY: 23336 AN XY: 73866

Gnomad4 AFR AF: 0.473

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.351

Gnomad4 EAS AF: 0.472

Gnomad4 SAS AF: 0.352

Gnomad4 FIN AF: 0.211

Gnomad4 NFE AF: 0.238

Gnomad4 OTH AF: 0.318

Alfa AF: 0.259 Hom.: 10874

Bravo AF: 0.327

Asia WGS AF: 0.421 AC: 1463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.25
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3811266; hg19: chr14-22747055;