rs16363

chr22-37013844-C-CTGTTTchr22-37013844-C-CTGTTTTGTTT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_003312.6(TST):c.596-2520_596-2519insAAACA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.58 in 151,378 control chromosomes in the GnomAD database, including 26,816 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.58 (26816 hom., cov: 0)
• Consequence: TST NM_003312.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207

Genes affected

TST (HGNC:12388): (thiosulfate sulfurtransferase) This is one of two neighboring genes encoding similar proteins that each contain two rhodanese domains. The encoded protein is localized to the mitochondria and catalyzes the conversion of thiosulfate and cyanide to thiocyanate and sulfite. In addition, the protein interacts with 5S ribosomal RNA and facilitates its import into the mitochondria. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2012]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TST	NM_003312.6	c.596-2520_596-2519insAAACA		intron_variant		ENST00000249042.8
TST	NM_001270483.1	c.596-2520_596-2519insAAACA		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TST	ENST00000249042.8	c.596-2520_596-2519insAAACA		intron_variant		1	NM_003312.6	P1
TST	ENST00000403892.7	c.596-2520_596-2519insAAACA		intron_variant		1		P1
TST	ENST00000622841.1	c.596-2520_596-2519insAAACA		intron_variant		5		P1

Frequencies

GnomAD3 genomes AF: 0.580 AC: 87768 AN: 151256 Hom.: 26787 Cov.: 0

Gnomad AFR AF: 0.775

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.580 AC: 87854 AN: 151378 Hom.: 26816 Cov.: 0 AF XY: 0.575 AC XY: 42506 AN XY: 73940

Gnomad4 AFR AF: 0.775

Gnomad4 AMR AF: 0.569

Gnomad4 ASJ AF: 0.587

Gnomad4 EAS AF: 0.527

Gnomad4 SAS AF: 0.495

Gnomad4 FIN AF: 0.431

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.585

Alfa AF: 0.287 Hom.: 396

Asia WGS AF: 0.495 AC: 1723 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16363; hg19: chr22-37409885;