rs2331601

Variant summary

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

The ENST00000656379.1(TRD-AS1):​n.270+94235T>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 0.777 in 150,962 control chromosomes in the GnomAD database, including 45,848 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 0.78 ( 45848 hom., cov: 25)

Consequence

TRD-AS1
ENST00000656379.1 intron, non_coding_transcript

Scores

1

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.941
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=-0.85).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.866 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+94235T>C intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.778
AC:
117291
AN:
150844
Hom.:
45817
Cov.:
25
show subpopulations
Gnomad AFR
AF:
0.699
Gnomad AMI
AF:
0.606
Gnomad AMR
AF:
0.835
Gnomad ASJ
AF:
0.785
Gnomad EAS
AF:
0.887
Gnomad SAS
AF:
0.817
Gnomad FIN
AF:
0.838
Gnomad MID
AF:
0.830
Gnomad NFE
AF:
0.793
Gnomad OTH
AF:
0.798
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.777
AC:
117369
AN:
150962
Hom.:
45848
Cov.:
25
AF XY:
0.783
AC XY:
57726
AN XY:
73732
show subpopulations
Gnomad4 AFR
AF:
0.699
Gnomad4 AMR
AF:
0.835
Gnomad4 ASJ
AF:
0.785
Gnomad4 EAS
AF:
0.887
Gnomad4 SAS
AF:
0.815
Gnomad4 FIN
AF:
0.838
Gnomad4 NFE
AF:
0.793
Gnomad4 OTH
AF:
0.801
Alfa
AF:
0.785
Hom.:
18416
Bravo
AF:
0.774

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
0.19

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: rs2331601; hg19: chr14-22774695; API