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11-67586499-T-C

Variant summary

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

The NM_000852.4(GSTP1):c.555T>C(p.Ser185=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 1,613,388 control chromosomes in the GnomAD database, including 104,195 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.38 ( 11609 hom., cov: 33)
Exomes 𝑓: 0.35 ( 92586 hom. )

Consequence

GSTP1
NM_000852.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.935
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=-0.94).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 11-67586499-T-C is Benign according to our data. Variant chr11-67586499-T-C is described in ClinVar as [Benign]. Clinvar id is 1281843.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=-0.935 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 = 0.483 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GSTP1NM_000852.4 linkuse as main transcriptc.555T>C p.Ser185= synonymous_variant 7/7 ENST00000398606.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GSTP1ENST00000398606.10 linkuse as main transcriptc.555T>C p.Ser185= synonymous_variant 7/71 NM_000852.4 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.379
AC:
57622
AN:
152076
Hom.:
11594
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.488
Gnomad AMI
AF:
0.380
Gnomad AMR
AF:
0.430
Gnomad ASJ
AF:
0.217
Gnomad EAS
AF:
0.177
Gnomad SAS
AF:
0.244
Gnomad FIN
AF:
0.273
Gnomad MID
AF:
0.256
Gnomad NFE
AF:
0.351
Gnomad OTH
AF:
0.371
GnomAD3 exomes
AF:
0.346
AC:
86223
AN:
249046
Hom.:
16434
AF XY:
0.334
AC XY:
45198
AN XY:
135140
show subpopulations
Gnomad AFR exome
AF:
0.495
Gnomad AMR exome
AF:
0.528
Gnomad ASJ exome
AF:
0.220
Gnomad EAS exome
AF:
0.176
Gnomad SAS exome
AF:
0.261
Gnomad FIN exome
AF:
0.281
Gnomad NFE exome
AF:
0.345
Gnomad OTH exome
AF:
0.345
GnomAD4 exome
AF:
0.350
AC:
511957
AN:
1461194
Hom.:
92586
Cov.:
38
AF XY:
0.346
AC XY:
251352
AN XY:
726954
show subpopulations
Gnomad4 AFR exome
AF:
0.497
Gnomad4 AMR exome
AF:
0.517
Gnomad4 ASJ exome
AF:
0.226
Gnomad4 EAS exome
AF:
0.160
Gnomad4 SAS exome
AF:
0.263
Gnomad4 FIN exome
AF:
0.285
Gnomad4 NFE exome
AF:
0.359
Gnomad4 OTH exome
AF:
0.343
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.379
AC:
57676
AN:
152194
Hom.:
11609
Cov.:
33
AF XY:
0.371
AC XY:
27600
AN XY:
74396
show subpopulations
Gnomad4 AFR
AF:
0.488
Gnomad4 AMR
AF:
0.430
Gnomad4 ASJ
AF:
0.217
Gnomad4 EAS
AF:
0.177
Gnomad4 SAS
AF:
0.244
Gnomad4 FIN
AF:
0.273
Gnomad4 NFE
AF:
0.351
Gnomad4 OTH
AF:
0.368
Alfa
AF:
0.351
Hom.:
11614
Bravo
AF:
0.401
Asia WGS
AF:
0.260
AC:
906
AN:
3478

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
-0.94
Cadd
Benign
0.62
Dann
Benign
0.26
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs4891; hg19: chr11-67353970; COSMIC: COSV66992478; COSMIC: COSV66992478; API