rs7069346

Variant names:

• chr10-122970360-T-A
• rs7069346
• XR_007062324.1:n.6150T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007062324.1(LOC124902519):​n.6150T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.664 in 151,894 control chromosomes in the GnomAD database, including 33,789 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 0.66 (33789 hom., cov: 31)
• Consequence: LOC124902519 XR_007062324.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.841
• Publications: 10 publications found

Genes affected

LOC124902519 (HGNC:):

PSTK (HGNC:28578): (phosphoseryl-tRNA kinase) Predicted to enable kinase activity and tRNA binding activity. Predicted to be involved in phosphorylation; selenocysteinyl-tRNA(Sec) biosynthetic process; and translation. Predicted to act upstream of or within selenocysteine incorporation. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000465232.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSTK	ENST00000465232.5	TSL:3	n.189-12912T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.664 AC: 100723 AN: 151776 Hom.: 33766 Cov.: 31

Gnomad AFR AF: 0.660

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.711

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.659

Gnomad NFE AF: 0.698

Gnomad OTH AF: 0.679

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.664 AC: 100791 AN: 151894 Hom.: 33789 Cov.: 31 AF XY: 0.659 AC XY: 48920 AN XY: 74216

African (AFR) AF: 0.660 AC: 27301 AN: 41390

American (AMR) AF: 0.601 AC: 9166 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.711 AC: 2468 AN: 3472

East Asian (EAS) AF: 0.414 AC: 2134 AN: 5158

South Asian (SAS) AF: 0.524 AC: 2522 AN: 4812

European-Finnish (FIN) AF: 0.708 AC: 7455 AN: 10532

Middle Eastern (MID) AF: 0.664 AC: 194 AN: 292

European-Non Finnish (NFE) AF: 0.697 AC: 47401 AN: 67962

Other (OTH) AF: 0.677 AC: 1425 AN: 2104

Alfa AF: 0.676 Hom.: 4320

Bravo AF: 0.657

Asia WGS AF: 0.514 AC: 1788 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.96
DANN	Benign	0.39
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs7069346; hg19: chr10-124729876;