GeneBe

14-22343205-G-A

Position:

Variant summary

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

The variant allele was found at a frequency of 0.296 in 150,732 control chromosomes in the GnomAD database, including 6,953 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 0.30 ( 6953 hom., cov: 26)

Consequence

TRA
intragenic

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.349
Variant links:
Genes affected

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 = 0.54 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TRA use as main transcriptn.22343205G>A intragenic_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TRD-AS1ENST00000656379.1 linkuse as main transcriptn.270+57839C>T intron_variant

Frequencies

GnomAD3 genomes
AF:
0.296
AC:
44605
AN:
150614
Hom.:
6947
Cov.:
26
show subpopulations
Gnomad AFR
AF:
0.256
Gnomad AMI
AF:
0.302
Gnomad AMR
AF:
0.275
Gnomad ASJ
AF:
0.311
Gnomad EAS
AF:
0.557
Gnomad SAS
AF:
0.483
Gnomad FIN
AF:
0.334
Gnomad MID
AF:
0.215
Gnomad NFE
AF:
0.286
Gnomad OTH
AF:
0.281
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.296
AC:
44640
AN:
150732
Hom.:
6953
Cov.:
26
AF XY:
0.302
AC XY:
22212
AN XY:
73602
show subpopulations
Gnomad4 AFR
AF:
0.256
Gnomad4 AMR
AF:
0.275
Gnomad4 ASJ
AF:
0.311
Gnomad4 EAS
AF:
0.557
Gnomad4 SAS
AF:
0.482
Gnomad4 FIN
AF:
0.334
Gnomad4 NFE
AF:
0.286
Gnomad4 OTH
AF:
0.284
Alfa
AF:
0.294
Hom.:
13622
Bravo
AF:
0.285
Asia WGS
AF:
0.495
AC:
1722
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
1.4
DANN
Benign
0.84

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: rs3811256; hg19: chr14-22811629; API