rs2297765

Variant names:

• chr1-165652970-C-A
• rs2297765
• NM_004528.4:c.249+935C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-165652970-C-A
• chr1-165652970-C-G
• chr1-165652970-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_004528.4(MGST3):​c.249+935C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: MGST3 NM_004528.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.77
• Publications: 3 publications found

Genes affected

MGST3 (HGNC:7064): (microsomal glutathione S-transferase 3) This gene encodes a member of the MAPEG (Membrane Associated Proteins in Eicosanoid and Glutathione metabolism) protein family. Members of this family are involved in the production of leukotrienes and prostaglandin E, important mediators of inflammation. This gene encodes an enzyme which catalyzes the conjugation of leukotriene A4 and reduced glutathione to produce leukotriene C4. This enzyme also demonstrates glutathione-dependent peroxidase activity towards lipid hydroperoxides.[provided by RefSeq, May 2011]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MGST3	NM_004528.4	c.249+935C>A		intron_variant	Intron 4 of 5	ENST00000367889.8	NP_004519.1
MGST3	XM_047421030.1	c.291+935C>A		intron_variant	Intron 5 of 6		XP_047276986.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MGST3	ENST00000367889.8	c.249+935C>A		intron_variant	Intron 4 of 5	1	NM_004528.4	ENSP00000356864.3
MGST3	ENST00000367883.3	c.291+935C>A		intron_variant	Intron 5 of 6	3		ENSP00000356858.1
MGST3	ENST00000367885.5	c.291+935C>A		intron_variant	Intron 5 of 6	2		ENSP00000356860.1
MGST3	ENST00000367884.6	c.249+935C>A		intron_variant	Intron 5 of 6	3		ENSP00000356859.1

Frequencies

GnomAD3 genomes Cov.: 33

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.038
DANN	Benign	0.38
PhyloP100		-2.8

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: rs2297765; hg19: chr1-165622207;