rs916048

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000656379.1(TRD-AS1):​n.270+78556G>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 0.391 in 150,178 control chromosomes in the GnomAD database, including 11,659 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 0.39 ( 11659 hom., cov: 25)

Consequence

TRD-AS1
ENST00000656379.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.455
Variant links:
Genes affected
TRD-AS1 (HGNC:56197): (TRD antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.97).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.502 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-AS1ENST00000656379.1 linkuse as main transcriptn.270+78556G>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.391
AC:
58699
AN:
150060
Hom.:
11659
Cov.:
25
show subpopulations
Gnomad AFR
AF:
0.412
Gnomad AMI
AF:
0.318
Gnomad AMR
AF:
0.342
Gnomad ASJ
AF:
0.412
Gnomad EAS
AF:
0.519
Gnomad SAS
AF:
0.469
Gnomad FIN
AF:
0.423
Gnomad MID
AF:
0.318
Gnomad NFE
AF:
0.370
Gnomad OTH
AF:
0.388
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.391
AC:
58732
AN:
150178
Hom.:
11659
Cov.:
25
AF XY:
0.396
AC XY:
29047
AN XY:
73296
show subpopulations
Gnomad4 AFR
AF:
0.411
Gnomad4 AMR
AF:
0.342
Gnomad4 ASJ
AF:
0.412
Gnomad4 EAS
AF:
0.519
Gnomad4 SAS
AF:
0.470
Gnomad4 FIN
AF:
0.423
Gnomad4 NFE
AF:
0.370
Gnomad4 OTH
AF:
0.387
Alfa
AF:
0.360
Hom.:
5687
Bravo
AF:
0.384
Asia WGS
AF:
0.503
AC:
1746
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
0.67
DANN
Benign
0.49

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs916048; hg19: chr14-22790920; API