7-143262206-G-T

Variant names:

• chr7-143262206-G-T
• rs1917760
• ENST00000436038.5:c.-18-942G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000436038.5(GSTK1):​c.-18-942G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0206 in 152,180 control chromosomes in the GnomAD database, including 222 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 0.021 (222 hom., cov: 32)
• Consequence: GSTK1 ENST00000436038.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.455
• Publications: 10 publications found

Genes affected

GSTK1 (HGNC:16906): (glutathione S-transferase kappa 1) This gene encodes a member of the kappa class of the glutathione transferase superfamily of enzymes that function in cellular detoxification. The encoded protein is localized to the peroxisome and catalyzes the conjugation of glutathione to a wide range of hydrophobic substates facilitating the removal of these compounds from cells. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Jan 2009]

TMEM139-AS1 (HGNC:40988): (TMEM139 antisense RNA 1)

LOC105375546 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM139-AS1	NR_133932.1	n.480-6785C>A		intron_variant	Intron 2 of 2
LOC105375546	XR_007060568.1	n.210-942G>T		intron_variant	Intron 2 of 2
LOC105375546	XR_007060569.1	n.244-942G>T		intron_variant	Intron 2 of 2
LOC105375546	XR_928072.4	n.231-942G>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GSTK1	ENST00000436038.5	c.-18-942G>T		intron_variant	Intron 1 of 4	5		ENSP00000408341.1
TMEM139-AS1	ENST00000427392.1	n.435-6785C>A		intron_variant	Intron 3 of 3	5
TMEM139-AS1	ENST00000446192.2	n.*198C>A		downstream_gene_variant		5

Frequencies

GnomAD3 genomes AF: 0.0205 AC: 3121 AN: 152062 Hom.: 220 Cov.: 32

Gnomad AFR AF: 0.00384

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.00850

Gnomad FIN AF: 0.00821

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000603

Gnomad OTH AF: 0.0268

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

GnomAD4 genome AF: 0.0206 AC: 3133 AN: 152180 Hom.: 222 Cov.: 32 AF XY: 0.0233 AC XY: 1734 AN XY: 74388

African (AFR) AF: 0.00383 AC: 159 AN: 41534

American (AMR) AF: 0.113 AC: 1728 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3466

East Asian (EAS) AF: 0.199 AC: 1024 AN: 5158

South Asian (SAS) AF: 0.00809 AC: 39 AN: 4818

European-Finnish (FIN) AF: 0.00821 AC: 87 AN: 10602

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000603 AC: 41 AN: 67998

Other (OTH) AF: 0.0260 AC: 55 AN: 2112

Alfa AF: 0.0127 Hom.: 146

Bravo AF: 0.0298

Asia WGS AF: 0.0810 AC: 279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.64
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs1917760; hg19: chr7-142959299;