chr14-22311424-A-G

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 0.486 in 150,620 control chromosomes in the GnomAD database, including 18,780 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 0.49 ( 18780 hom., cov: 26)

Consequence

TRA
intragenic

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.10
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 (Cadd=7.903).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TRA n.22311424A>G intragenic_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TRD-AS1ENST00000656379.1 linkn.270+89620T>C intron_variant

Frequencies

GnomAD3 genomes
AF:
0.487
AC:
73226
AN:
150502
Hom.:
18773
Cov.:
26
show subpopulations
Gnomad AFR
AF:
0.323
Gnomad AMI
AF:
0.388
Gnomad AMR
AF:
0.591
Gnomad ASJ
AF:
0.449
Gnomad EAS
AF:
0.738
Gnomad SAS
AF:
0.563
Gnomad FIN
AF:
0.522
Gnomad MID
AF:
0.472
Gnomad NFE
AF:
0.535
Gnomad OTH
AF:
0.512
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.486
AC:
73245
AN:
150620
Hom.:
18780
Cov.:
26
AF XY:
0.491
AC XY:
36100
AN XY:
73564
show subpopulations
Gnomad4 AFR
AF:
0.323
Gnomad4 AMR
AF:
0.591
Gnomad4 ASJ
AF:
0.449
Gnomad4 EAS
AF:
0.738
Gnomad4 SAS
AF:
0.560
Gnomad4 FIN
AF:
0.522
Gnomad4 NFE
AF:
0.535
Gnomad4 OTH
AF:
0.509
Alfa
AF:
0.527
Hom.:
25515
Bravo
AF:
0.484

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
CADD
Benign
7.9

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: rs7146411; hg19: -; API