rs17593068

Variant names:

• chr11-67583461-G-T
• rs17593068
• ENST00000906565.1:c.-383G>T

Your query was ambiguous. Multiple possible variants found:

• chr11-67583461-G-T
• chr11-67583461-G-A

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The ENST00000906565.1(GSTP1):​c.-383G>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 203,320 control chromosomes in the GnomAD database, including 15,119 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.37 (11016 hom., cov: 32)
  • Exomes 𝑓: 0.38 (4103 hom.)
• Consequence: GSTP1 ENST00000906565.1 upstream_gene
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.249
• Publications: 17 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 11-67583461-G-T is Benign according to our data. Variant chr11-67583461-G-T is described in ClinVar as Benign. ClinVar VariationId is 1237952.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000906565.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSTP1	ENST00000906565.1		c.-383G>T		upstream_gene	N/A	ENSP00000576624.1
	GSTP1	ENST00000914374.1		c.-383G>T		upstream_gene	N/A	ENSP00000584433.1
	GSTP1	ENST00000914373.1		c.-383G>T		upstream_gene	N/A	ENSP00000584432.1

Frequencies

GnomAD3 genomes AF: 0.373 AC: 56574 AN: 151606 Hom.: 11015 Cov.: 32

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.369

GnomAD4 exome AF: 0.381 AC: 19675 AN: 51610 Hom.: 4103 AF XY: 0.382 AC XY: 9982 AN XY: 26120

African (AFR) AF: 0.381 AC: 696 AN: 1828

American (AMR) AF: 0.256 AC: 336 AN: 1310

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 589 AN: 2144

East Asian (EAS) AF: 0.150 AC: 631 AN: 4204

South Asian (SAS) AF: 0.311 AC: 156 AN: 502

European-Finnish (FIN) AF: 0.333 AC: 1110 AN: 3330

Middle Eastern (MID) AF: 0.335 AC: 95 AN: 284

European-Non Finnish (NFE) AF: 0.428 AC: 14709 AN: 34368

Other (OTH) AF: 0.372 AC: 1353 AN: 3640

GnomAD4 genome AF: 0.373 AC: 56592 AN: 151710 Hom.: 11016 Cov.: 32 AF XY: 0.362 AC XY: 26840 AN XY: 74112

African (AFR) AF: 0.381 AC: 15759 AN: 41378

American (AMR) AF: 0.277 AC: 4221 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 904 AN: 3470

East Asian (EAS) AF: 0.158 AC: 816 AN: 5158

South Asian (SAS) AF: 0.294 AC: 1413 AN: 4804

European-Finnish (FIN) AF: 0.320 AC: 3346 AN: 10472

Middle Eastern (MID) AF: 0.325 AC: 95 AN: 292

European-Non Finnish (NFE) AF: 0.426 AC: 28915 AN: 67860

Other (OTH) AF: 0.366 AC: 772 AN: 2110

Alfa AF: 0.328 Hom.: 1581

Bravo AF: 0.370

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.9
DANN	Benign	0.57
PhyloP100		0.25
PromoterAI		0.44	Neutral

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs17593068; hg19: chr11-67350932; COSMIC: COSV66992393;