8-52160693-C-T

Position:

• chr8-52160693-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.1594+682G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 152,006 control chromosomes in the GnomAD database, including 13,923 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 0.41 (13923 hom., cov: 33)
• Consequence: ST18 NM_001352837.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ST18	NM_001352837.2	c.1594+682G>A		intron_variant		ENST00000689386.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ST18	ENST00000689386.1	c.1594+682G>A		intron_variant			NM_001352837.2	P1

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62644 AN: 151888 Hom.: 13906 Cov.: 33

Gnomad AFR AF: 0.595

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.413 AC: 62705 AN: 152006 Hom.: 13923 Cov.: 33 AF XY: 0.409 AC XY: 30409 AN XY: 74300

Gnomad4 AFR AF: 0.595

Gnomad4 AMR AF: 0.313

Gnomad4 ASJ AF: 0.324

Gnomad4 EAS AF: 0.334

Gnomad4 SAS AF: 0.384

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.343

Gnomad4 OTH AF: 0.360

Alfa AF: 0.381 Hom.: 2154

Bravo AF: 0.413

Asia WGS AF: 0.387 AC: 1349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.19
DANN	Benign	0.52

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: rs1365245; hg19: chr8-53073253; COSMIC: COSV52483824;