rs16363

Variant names:

• chr22-37013844-C-CTGTTT
• rs16363
• NM_003312.6:c.596-2524_596-2520dupAAACA

Your query was ambiguous. Multiple possible variants found:

• chr22-37013844-C-CTGTTT
• chr22-37013844-C-CTGTTTTGTTT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_003312.6(TST):​c.596-2524_596-2520dupAAACA variant causes a intron change involving the alteration of a non-conserved nucleotide. 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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TST	NM_003312.6	c.596-2524_596-2520dupAAACA		intron_variant	Intron 2 of 2	ENST00000249042.8	NP_003303.2
TST	NM_001270483.1	c.596-2524_596-2520dupAAACA		intron_variant	Intron 2 of 2		NP_001257412.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TST	ENST00000249042.8	c.596-2520_596-2519insAAACA		intron_variant	Intron 2 of 2	1	NM_003312.6	ENSP00000249042.3
TST	ENST00000403892.7	c.596-2520_596-2519insAAACA		intron_variant	Intron 1 of 1	1		ENSP00000385828.3
TST	ENST00000622841.1	c.596-2520_596-2519insAAACA		intron_variant	Intron 2 of 2	5		ENSP00000478739.1

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

African (AFR) AF: 0.775 AC: 31908 AN: 41180

American (AMR) AF: 0.569 AC: 8658 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.587 AC: 2030 AN: 3458

East Asian (EAS) AF: 0.527 AC: 2703 AN: 5130

South Asian (SAS) AF: 0.495 AC: 2382 AN: 4810

European-Finnish (FIN) AF: 0.431 AC: 4514 AN: 10462

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.497 AC: 33735 AN: 67824

Other (OTH) AF: 0.585 AC: 1227 AN: 2098

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

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.21
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs16363; hg19: chr22-37409885;