rs1871041

Variant names:

• chr11-67584069-A-G
• rs1871041
• NM_000852.4:c.2-65A>G

Your query was ambiguous. Multiple possible variants found:

• chr11-67584069-A-G
• chr11-67584069-A-T

Variant summary

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

The NM_000852.4(GSTP1):​c.2-65A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.909 in 1,373,348 control chromosomes in the GnomAD database, including 567,608 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.89 (59760 hom., cov: 32)
  • Exomes 𝑓: 0.91 (507848 hom.)
• Consequence: GSTP1 NM_000852.4 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.580
• Publications: 9 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 11-67584069-A-G is Benign according to our data. Variant chr11-67584069-A-G is described in ClinVar as Benign. ClinVar VariationId is 1274091.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.911 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GSTP1	NM_000852.4	c.2-65A>G		intron_variant	Intron 1 of 6	ENST00000398606.10	NP_000843.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GSTP1	ENST00000398606.10	c.2-65A>G		intron_variant	Intron 1 of 6	1	NM_000852.4	ENSP00000381607.3

Frequencies

GnomAD3 genomes AF: 0.887 AC: 134470 AN: 151622 Hom.: 59739 Cov.: 32

Gnomad AFR AF: 0.841

Gnomad AMI AF: 0.939

Gnomad AMR AF: 0.892

Gnomad ASJ AF: 0.909

Gnomad EAS AF: 0.873

Gnomad SAS AF: 0.925

Gnomad FIN AF: 0.838

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.917

Gnomad OTH AF: 0.900

GnomAD4 exome AF: 0.911 AC: 1113182 AN: 1221610 Hom.: 507848 Cov.: 17 AF XY: 0.912 AC XY: 561892 AN XY: 616036

African (AFR) AF: 0.842 AC: 25526 AN: 30330

American (AMR) AF: 0.896 AC: 36660 AN: 40896

Ashkenazi Jewish (ASJ) AF: 0.914 AC: 21834 AN: 23880

East Asian (EAS) AF: 0.833 AC: 30909 AN: 37090

South Asian (SAS) AF: 0.922 AC: 72322 AN: 78438

European-Finnish (FIN) AF: 0.843 AC: 43033 AN: 51052

Middle Eastern (MID) AF: 0.925 AC: 3604 AN: 3898

European-Non Finnish (NFE) AF: 0.920 AC: 832005 AN: 904074

Other (OTH) AF: 0.910 AC: 47289 AN: 51952

GnomAD4 genome AF: 0.887 AC: 134546 AN: 151738 Hom.: 59760 Cov.: 32 AF XY: 0.885 AC XY: 65630 AN XY: 74122

African (AFR) AF: 0.841 AC: 34839 AN: 41422

American (AMR) AF: 0.891 AC: 13637 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.909 AC: 3151 AN: 3466

East Asian (EAS) AF: 0.872 AC: 4403 AN: 5048

South Asian (SAS) AF: 0.923 AC: 4449 AN: 4818

European-Finnish (FIN) AF: 0.838 AC: 8807 AN: 10512

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.917 AC: 62244 AN: 67852

Other (OTH) AF: 0.899 AC: 1898 AN: 2112

Alfa AF: 0.903 Hom.: 9120

Bravo AF: 0.889

Asia WGS AF: 0.898 AC: 3122 AN: 3474

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Nov 12, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.0
DANN	Benign	0.58
PhyloP100		0.58
PromoterAI		0.012	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1871041; hg19: chr11-67351540;