rs140289

Variant summary

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

The XM_024452202.2(GSTT4):​c.472-4918A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.671 in 145,860 control chromosomes in the GnomAD database, including 28,763 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 0.67 ( 28763 hom., cov: 34)

Consequence

GSTT4
XM_024452202.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.01
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=-1.0).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GSTT4XM_024452202.2 linkuse as main transcriptc.472-4918A>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.670
AC:
97705
AN:
145750
Hom.:
28720
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.798
Gnomad AMI
AF:
0.662
Gnomad AMR
AF:
0.632
Gnomad ASJ
AF:
0.657
Gnomad EAS
AF:
0.500
Gnomad SAS
AF:
0.654
Gnomad FIN
AF:
0.648
Gnomad MID
AF:
0.684
Gnomad NFE
AF:
0.620
Gnomad OTH
AF:
0.672
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.671
AC:
97803
AN:
145860
Hom.:
28763
Cov.:
34
AF XY:
0.670
AC XY:
47698
AN XY:
71240
show subpopulations
Gnomad4 AFR
AF:
0.798
Gnomad4 AMR
AF:
0.632
Gnomad4 ASJ
AF:
0.657
Gnomad4 EAS
AF:
0.500
Gnomad4 SAS
AF:
0.655
Gnomad4 FIN
AF:
0.648
Gnomad4 NFE
AF:
0.620
Gnomad4 OTH
AF:
0.671
Alfa
AF:
0.757
Hom.:
14292
Asia WGS
AF:
0.685
AC:
2384
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
2.1
DANN
Benign
0.34

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: rs140289; hg19: chr22-24336327; API