rs10483271

chr14-22293365-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.271-91983C>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 0.281 in 151,094 control chromosomes in the GnomAD database, including 6,417 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 0.28 (6417 hom., cov: 27)
• Consequence: TRD-AS1 ENST00000656379.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.208

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.378 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.271-91983C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42465 AN: 150976 Hom.: 6405 Cov.: 27

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.281 AC: 42513 AN: 151094 Hom.: 6417 Cov.: 27 AF XY: 0.276 AC XY: 20326 AN XY: 73770

Gnomad4 AFR AF: 0.383

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.229

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.268

Alfa AF: 0.268 Hom.: 2881

Bravo AF: 0.279

Asia WGS AF: 0.165 AC: 578 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.84
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10483271; hg19: chr14-22761250;