Genetic Variant NM_001113207.2: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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
TSTD1	NM_001113207.2 link	c.11-72G>C	intron_variant	Intron 1 of 3	ENST00000423014.3	NP_001106678.1	Q8NFU3-1
TSTD1	NM_001113205.2 link	c.11-72G>C	intron_variant	Intron 1 of 2		NP_001106676.1	Q8NFU3-3
TSTD1	NM_001113206.2 link	c.10+135G>C	intron_variant	Intron 1 of 2		NP_001106677.1	Q8NFU3-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TSTD1	ENST00000423014.3 link	c.11-72G>C		intron_variant	Intron 1 of 3	2	NM_001113207.2	ENSP00000388293.2		Q8NFU3-1
ENSG00000270149	ENST00000289779.7 link	n.10+135G>C		intron_variant	Intron 1 of 12	2		ENSP00000289779.4		A0A0A0MQY5

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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over