chr8-52423117-C-T

Variant names:

• chr8-52423117-C-T
• rs716583
• ENST00000523652.1:n.76-13665G>A

Variant summary

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

The ENST00000523652.1(ST18):​n.76-13665G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.727 in 152,160 control chromosomes in the GnomAD database, including 40,485 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 0.73 (40485 hom., cov: 33)
• Consequence: ST18 ENST00000523652.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550
• Publications: 5 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.79 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ST18	ENST00000523652.1	n.76-13665G>A		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.727 AC: 110584 AN: 152042 Hom.: 40474 Cov.: 33

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.759

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.712

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

GnomAD4 genome AF: 0.727 AC: 110648 AN: 152160 Hom.: 40485 Cov.: 33 AF XY: 0.723 AC XY: 53741 AN XY: 74372

African (AFR) AF: 0.798 AC: 33105 AN: 41504

American (AMR) AF: 0.699 AC: 10681 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.642 AC: 2228 AN: 3472

East Asian (EAS) AF: 0.759 AC: 3917 AN: 5160

South Asian (SAS) AF: 0.685 AC: 3305 AN: 4822

European-Finnish (FIN) AF: 0.665 AC: 7040 AN: 10584

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.709 AC: 48242 AN: 68010

Other (OTH) AF: 0.708 AC: 1499 AN: 2116

Alfa AF: 0.713 Hom.: 162173

Bravo AF: 0.731

Asia WGS AF: 0.664 AC: 2309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.4
DANN	Benign	0.46
PhyloP100		-0.055

Splicing

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

Other links and lift over

dbSNP: rs716583; hg19: chr8-53335677;