Variant 1-161037944-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001113207.2(TSTD1):c.265A>C(p.Thr89Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000357 in 1,399,484 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0000036 ( 0 hom. )

Consequence

TSTD1
NM_001113207.2 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.17

Variant links:

Genes affected

TSTD1 (HGNC:35410): (thiosulfate sulfurtransferase like domain containing 1) Predicted to enable thiosulfate-thiol sulfurtransferase activity. Predicted to be involved in sulfide oxidation, using sulfide:quinone oxidoreductase. Located in cytoplasmic ribonucleoprotein granule and cytosol. [provided by Alliance of Genome Resources, Apr 2022]

TSTD1 links:

ENSG00000270149 (HGNC:):

ENSG00000270149 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TSTD1	NM_001113207.2 linkuse as main transcript	c.265A>C	p.Thr89Pro	missense_variant	3/4	ENST00000423014.3	NP_001106678.1	Q8NFU3-1
TSTD1	NM_001113205.2 linkuse as main transcript	c.265A>C	p.Thr89Pro	missense_variant	3/3		NP_001106676.1	Q8NFU3-3
TSTD1	NM_001113206.2 linkuse as main transcript	c.142A>C	p.Thr48Pro	missense_variant	2/3		NP_001106677.1	Q8NFU3-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TSTD1	ENST00000423014.3 linkuse as main transcript	c.265A>C	p.Thr89Pro	missense_variant	3/4	2	NM_001113207.2	ENSP00000388293.2		Q8NFU3-1
ENSG00000270149	ENST00000289779.7 linkuse as main transcript	n.10+936A>C		intron_variant		2		ENSP00000289779.4		A0A0A0MQY5

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.0000128

AC:

AN:

156762

Hom.:

AF XY:

0.0000120

AC XY:

AN XY:

83070

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000330

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000357

AC:

AN:

1399484

Hom.:

Cov.:

AF XY:

0.00000290

AC XY:

AN XY:

690246

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000278

Gnomad4 OTH exome

AF:

0.0000345

GnomAD4 genome

Cov.:

Bravo

AF:

0.00000756

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

May 09, 2024

The c.265A>C (p.T89P) alteration is located in exon 3 (coding exon 3) of the TSTD1 gene. This alteration results from a A to C substitution at nucleotide position 265, causing the threonine (T) at amino acid position 89 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.79

BayesDel_addAF

Benign

-0.0066

BayesDel_noAF

Benign

-0.24

CADD

Benign

DANN

Uncertain

0.98

DEOGEN2

Benign

0.25

.;.;.;T;T

Eigen

Benign

0.022

Eigen_PC

Benign

-0.079

FATHMM_MKL

Benign

0.57

LIST_S2

Benign

0.64

T;T;T;T;T

M_CAP

Benign

0.028

MetaRNN

Uncertain

0.72

D;D;D;D;D

MetaSVM

Benign

-1.1

MutationAssessor

Uncertain

2.6

M;.;.;M;.

PROVEAN

Uncertain

-2.8

D;D;D;D;.

REVEL

Benign

0.29

Sift

Uncertain

0.0090

D;T;D;D;.

Sift4G

Benign

0.17

T;T;T;T;D

Polyphen

0.96

D;.;P;P;.

Vest4

0.55

MutPred

0.77

Loss of MoRF binding (P = 0.0582);.;.;Loss of MoRF binding (P = 0.0582);.;

MVP

0.040

ClinPred

0.84

GERP RS

2.8

Varity_R

0.74

gMVP

0.91

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over