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11-67584690-C-T

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_000852.4(GSTP1):c.150C>T(p.Tyr50=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00904 in 1,613,170 control chromosomes in the GnomAD database, including 1,168 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.049 ( 595 hom., cov: 33)
Exomes 𝑓: 0.0049 ( 573 hom. )

Consequence

GSTP1
NM_000852.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.05
Variant links:
Genes affected
GSTP1 (HGNC:4638): (glutathione S-transferase pi 1) Glutathione S-transferases (GSTs) are a family of enzymes that play an important role in detoxification by catalyzing the conjugation of many hydrophobic and electrophilic compounds with reduced glutathione. Based on their biochemical, immunologic, and structural properties, the soluble GSTs are categorized into 4 main classes: alpha, mu, pi, and theta. This GST family member is a polymorphic gene encoding active, functionally different GSTP1 variant proteins that are thought to function in xenobiotic metabolism and play a role in susceptibility to cancer, and other diseases. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 11-67584690-C-T is Benign according to our data. Variant chr11-67584690-C-T is described in ClinVar as [Benign]. Clinvar id is 1269062.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-1.05 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GSTP1NM_000852.4 linkuse as main transcriptc.150C>T p.Tyr50= synonymous_variant 4/7 ENST00000398606.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GSTP1ENST00000398606.10 linkuse as main transcriptc.150C>T p.Tyr50= synonymous_variant 4/71 NM_000852.4 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0487
AC:
7415
AN:
152148
Hom.:
596
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.169
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0188
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000559
Gnomad OTH
AF:
0.0392
GnomAD3 exomes
AF:
0.0119
AC:
2962
AN:
249016
Hom.:
229
AF XY:
0.00841
AC XY:
1137
AN XY:
135182
show subpopulations
Gnomad AFR exome
AF:
0.170
Gnomad AMR exome
AF:
0.00760
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000196
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000443
Gnomad OTH exome
AF:
0.00447
GnomAD4 exome
AF:
0.00490
AC:
7165
AN:
1460904
Hom.:
573
Cov.:
32
AF XY:
0.00409
AC XY:
2969
AN XY:
726790
show subpopulations
Gnomad4 AFR exome
AF:
0.176
Gnomad4 AMR exome
AF:
0.00874
Gnomad4 ASJ exome
AF:
0.0000383
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000220
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000261
Gnomad4 OTH exome
AF:
0.00933
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0488
AC:
7424
AN:
152266
Hom.:
595
Cov.:
33
AF XY:
0.0461
AC XY:
3434
AN XY:
74448
show subpopulations
Gnomad4 AFR
AF:
0.169
Gnomad4 AMR
AF:
0.0188
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000559
Gnomad4 OTH
AF:
0.0388
Alfa
AF:
0.0165
Hom.:
98
Bravo
AF:
0.0547
Asia WGS
AF:
0.00577
AC:
20
AN:
3478
EpiCase
AF:
0.000327
EpiControl
AF:
0.000533

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxJun 09, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
Cadd
Benign
7.4
Dann
Benign
0.74
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
Details are displayed if max score is > 0.2

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: rs8191448; hg19: chr11-67352161; API