rs2360808

Positions:

• chr8-52213340-C-T

Variant summary

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

The NM_001352837.2(ST18):​c.55+863G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 151,786 control chromosomes in the GnomAD database, including 2,852 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 0.13 (2852 hom., cov: 31)
• Consequence: ST18 NM_001352837.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.01

Genes affected

ST18 (HGNC:18695): (ST18 C2H2C-type zinc finger transcription factor) Enables RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in cytokine-mediated signaling pathway; negative regulation of cell population proliferation; and positive regulation of nitrogen compound metabolic process. Located in nucleus. Part of protein-DNA complex. [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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.35 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ST18	NM_001352837.2	c.55+863G>A		intron_variant		ENST00000689386.1	NP_001339766.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ST18	ENST00000689386.1	c.55+863G>A		intron_variant			NM_001352837.2	ENSP00000509475	P1

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19163 AN: 151668 Hom.: 2837 Cov.: 31

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.0288

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.0488

Gnomad FIN AF: 0.0570

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0163

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.127 AC: 19223 AN: 151786 Hom.: 2852 Cov.: 31 AF XY: 0.128 AC XY: 9494 AN XY: 74164

Gnomad4 AFR AF: 0.355

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.0288

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.0476

Gnomad4 FIN AF: 0.0570

Gnomad4 NFE AF: 0.0163

Gnomad4 OTH AF: 0.109

Alfa AF: 0.0364 Hom.: 774

Bravo AF: 0.141

Asia WGS AF: 0.106 AC: 367 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.019
DANN	Benign	0.55

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: rs2360808; hg19: chr8-53125900;