Genetic Variant TSTD1:c.11-72G>C (chr1-161038745-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001113207.2(TSTD1):c.11-72G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 1,520,862 control chromosomes in the GnomAD database, including 11,076 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 0.11 ( 984 hom., cov: 32)

Exomes 𝑓: 0.12 ( 10092 hom. )

Consequence

TSTD1
NM_001113207.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0650

Publications

31 publications found

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 was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001113207.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
TSTD1	NM_001113207.2	MANE Select	c.11-72G>C	intron	N/A	NP_001106678.1
TSTD1	NM_001113205.2		c.11-72G>C	intron	N/A	NP_001106676.1
TSTD1	NM_001113206.2		c.10+135G>C	intron	N/A	NP_001106677.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
TSTD1	ENST00000423014.3	TSL:2 MANE Select	c.11-72G>C	intron	N/A	ENSP00000388293.2
TSTD1	ENST00000318289.14	TSL:1	c.11-72G>C	intron	N/A	ENSP00000325518.10
ENSG00000270149	ENST00000289779.7	TSL:2	n.10+135G>C	intron	N/A	ENSP00000289779.4

Frequencies

GnomAD3 genomes

AF:

0.110

AC:

16737

AN:

152096

Hom.:

983

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0826

Gnomad AMI

AF:

0.124

Gnomad AMR

AF:

0.120

Gnomad ASJ

AF:

0.149

Gnomad EAS

AF:

0.00135

Gnomad SAS

AF:

0.0582

Gnomad FIN

AF:

0.141

Gnomad MID

AF:

0.146

Gnomad NFE

AF:

0.129

Gnomad OTH

AF:

0.111

GnomAD4 exome

AF:

0.117

AC:

159972

AN:

1368648

Hom.:

10092

Cov.:

AF XY:

0.116

AC XY:

77264

AN XY:

668684

show subpopulations

African (AFR)

AF:

0.0826

AC:

2564

AN:

31024

American (AMR)

AF:

0.0951

AC:

3289

AN:

34574

Ashkenazi Jewish (ASJ)

AF:

0.151

AC:

3674

AN:

24280

East Asian (EAS)

AF:

0.00243

AC:

AN:

34956

South Asian (SAS)

AF:

0.0651

AC:

5061

AN:

77738

European-Finnish (FIN)

AF:

0.142

AC:

6912

AN:

48656

Middle Eastern (MID)

AF:

0.119

AC:

659

AN:

5544

European-Non Finnish (NFE)

AF:

0.124

AC:

131222

AN:

1055398

Other (OTH)

AF:

0.115

AC:

6506

AN:

56478

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

8193

16386

24578

32771

40964

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4794

9588

14382

19176

23970

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.110

AC:

16743

AN:

152214

Hom.:

984

Cov.:

AF XY:

0.109

AC XY:

8138

AN XY:

74426

show subpopulations

African (AFR)

AF:

0.0826

AC:

3429

AN:

41528

American (AMR)

AF:

0.120

AC:

1834

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.149

AC:

518

AN:

3468

East Asian (EAS)

AF:

0.00135

AC:

AN:

5176

South Asian (SAS)

AF:

0.0586

AC:

283

AN:

4828

European-Finnish (FIN)

AF:

0.141

AC:

1496

AN:

10614

Middle Eastern (MID)

AF:

0.146

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.129

AC:

8786

AN:

67994

Other (OTH)

AF:

0.111

AC:

234

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

764

1528

2293

3057

3821

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

190

380

570

760

950

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.118

Hom.:

148

Bravo

AF:

0.106

Asia WGS

AF:

0.0460

AC:

159

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

(source)

DANN

Benign

0.83

PhyloP100

-0.065

PromoterAI

0.30

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over