Variant rs16363 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.207

Variant links:

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]

TST links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

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	Protein	UniProt
TST	NM_003312.6 linkuse as main transcript	c.596-2524_596-2520dupAAACA		intron_variant		ENST00000249042.8	NP_003303.2	Q16762A0A384NKQ2
TST	NM_001270483.1 linkuse as main transcript	c.596-2524_596-2520dupAAACA		intron_variant			NP_001257412.1	Q16762A0A384NKQ2

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
TST	ENST00000249042.8 linkuse as main transcript	c.596-2524_596-2520dupAAACA	intron_variant	1	NM_003312.6	ENSP00000249042.3	Q16762
TST	ENST00000403892.7 linkuse as main transcript	c.596-2524_596-2520dupAAACA	intron_variant	1		ENSP00000385828.3	Q16762
TST	ENST00000622841.1 linkuse as main transcript	c.596-2524_596-2520dupAAACA	intron_variant	5		ENSP00000478739.1	Q16762

Frequencies

GnomAD3 genomes

AF:

0.580

AC:

87768

AN:

151256

Hom.:

26787

Cov.:

show subpopulations

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.:

AF XY:

0.575

AC XY:

42506

AN XY:

73940

show subpopulations

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

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over