rs2164624

chr10-104253687-G-Achr10-104253687-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007062284.1(LOC124902497):n.366-5095C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 152,090 control chromosomes in the GnomAD database, including 5,550 homozygotes. 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: 𝑓 0.25 (5550 hom., cov: 32)
• Consequence: LOC124902497 XR_007062284.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190

Genes affected

LOC124902497 (HGNC:):

GSTO1 (HGNC:13312): (glutathione S-transferase omega 1) The protein encoded by this gene is an omega class glutathione S-transferase (GST) with glutathione-dependent thiol transferase and dehydroascorbate reductase activities. GSTs are involved in the metabolism of xenobiotics and carcinogens. The encoded protein acts as a homodimer and is found in the cytoplasm. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902497	XR_007062284.1	n.366-5095C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GSTO1	ENST00000470554.5	n.106-777G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38386 AN: 151972 Hom.: 5547 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.253 AC: 38404 AN: 152090 Hom.: 5550 Cov.: 32 AF XY: 0.250 AC XY: 18562 AN XY: 74326

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.404

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.228

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.332

Gnomad4 OTH AF: 0.288

Alfa AF: 0.270 Hom.: 884

Bravo AF: 0.245

Asia WGS AF: 0.187 AC: 650 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
Cadd	Benign	2.0
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2164624; hg19: chr10-106013445;