rs10908821

Variant names:

• chr1-161038745-C-A
• rs10908821
• NM_001113207.2:c.11-72G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-161038745-C-A
• chr1-161038745-C-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001113207.2(TSTD1):​c.11-72G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: TSTD1 NM_001113207.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0650
• Publications: 0 publications found

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

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).

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

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	12
DANN	Benign	0.87
PhyloP100		-0.065
PromoterAI		0.25	Neutral

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

Other links and lift over

dbSNP: rs10908821; hg19: chr1-161008535;