GeneBe

rs12436199

Positions:

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 0.782 in 150,760 control chromosomes in the GnomAD database, including 46,347 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 ( 46347 hom., cov: 25)

Consequence

TRA
intragenic

Scores

1

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.737
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=-0.93).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TRA use as main transcriptn.22348733A>G intragenic_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TRD-AS1ENST00000656379.1 linkuse as main transcriptn.270+52311T>C intron_variant

Frequencies

GnomAD3 genomes
AF:
0.782
AC:
117732
AN:
150642
Hom.:
46305
Cov.:
25
show subpopulations
Gnomad AFR
AF:
0.867
Gnomad AMI
AF:
0.829
Gnomad AMR
AF:
0.709
Gnomad ASJ
AF:
0.663
Gnomad EAS
AF:
0.822
Gnomad SAS
AF:
0.813
Gnomad FIN
AF:
0.731
Gnomad MID
AF:
0.639
Gnomad NFE
AF:
0.756
Gnomad OTH
AF:
0.752
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.782
AC:
117832
AN:
150760
Hom.:
46347
Cov.:
25
AF XY:
0.779
AC XY:
57302
AN XY:
73562
show subpopulations
Gnomad4 AFR
AF:
0.867
Gnomad4 AMR
AF:
0.709
Gnomad4 ASJ
AF:
0.663
Gnomad4 EAS
AF:
0.822
Gnomad4 SAS
AF:
0.812
Gnomad4 FIN
AF:
0.731
Gnomad4 NFE
AF:
0.756
Gnomad4 OTH
AF:
0.755
Alfa
AF:
0.755
Hom.:
20365
Bravo
AF:
0.783

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
1.8

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: rs12436199; hg19: chr14-22817156; API