rs7069346

Positions:

• chr10-122970360-T-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902519	XR_007062324.1	n.6150T>A		non_coding_transcript_exon_variant	3/3
LOC124902519	XR_007062325.1	n.6082T>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PSTK	ENST00000465232.5	n.189-12912T>A		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.660

Gnomad4 AMR AF: 0.601

Gnomad4 ASJ AF: 0.711

Gnomad4 EAS AF: 0.414

Gnomad4 SAS AF: 0.524

Gnomad4 FIN AF: 0.708

Gnomad4 NFE AF: 0.697

Gnomad4 OTH AF: 0.677

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7069346; hg19: chr10-124729876;