1-161038745-C-G

Position:

• chr1-161038745-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0650

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]

ENSG00000270149 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TSTD1	NM_001113207.2	c.11-72G>C		intron_variant		ENST00000423014.3	NP_001106678.1
TSTD1	NM_001113205.2	c.11-72G>C		intron_variant			NP_001106676.1
TSTD1	NM_001113206.2	c.10+135G>C		intron_variant			NP_001106677.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TSTD1	ENST00000423014.3	c.11-72G>C		intron_variant		2	NM_001113207.2	ENSP00000388293.2
ENSG00000270149	ENST00000289779.7	n.10+135G>C		intron_variant		2		ENSP00000289779.4

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16737 AN: 152096 Hom.: 983 Cov.: 32

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.: 32 AF XY: 0.116 AC XY: 77264 AN XY: 668684

Gnomad4 AFR exome AF: 0.0826

Gnomad4 AMR exome AF: 0.0951

Gnomad4 ASJ exome AF: 0.151

Gnomad4 EAS exome AF: 0.00243

Gnomad4 SAS exome AF: 0.0651

Gnomad4 FIN exome AF: 0.142

Gnomad4 NFE exome AF: 0.124

Gnomad4 OTH exome AF: 0.115

GnomAD4 genome AF: 0.110 AC: 16743 AN: 152214 Hom.: 984 Cov.: 32 AF XY: 0.109 AC XY: 8138 AN XY: 74426

Gnomad4 AFR AF: 0.0826

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0586

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.111

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	12
DANN	Benign	0.83

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

LitVar

Other links and lift over

dbSNP: rs10908821; hg19: chr1-161008535;