7-143262206-G-T

Position:

• chr7-143262206-G-T

Variant summary

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

The NR_133932.1(TMEM139-AS1):​n.480-6785C>A 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 0.0206 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: TMEM139-AS1 NR_133932.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.455

Genes affected

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

LOC105375546 (HGNC:):

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
TMEM139-AS1	NR_133932.1	n.480-6785C>A		intron_variant, non_coding_transcript_variant
LOC105375546	XR_007060569.1	n.244-942G>T		intron_variant, non_coding_transcript_variant
LOC105375546	XR_007060568.1	n.210-942G>T		intron_variant, non_coding_transcript_variant
LOC105375546	XR_928072.4	n.231-942G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM139-AS1	ENST00000427392.1	n.435-6785C>A		intron_variant, non_coding_transcript_variant		5
GSTK1	ENST00000436038.5	c.-18-942G>T		intron_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

Gnomad4 AFR AF: 0.00383

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.199

Gnomad4 SAS AF: 0.00809

Gnomad4 FIN AF: 0.00821

Gnomad4 NFE AF: 0.000603

Gnomad4 OTH AF: 0.0260

Alfa AF: 0.00946 Hom.: 99

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1917760; hg19: chr7-142959299;