rs2360806

chr8-52213174-A-C

Variant summary

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

The NM_001352837.2(ST18):c.55+1029T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 152,074 control chromosomes in the GnomAD database, including 4,825 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 0.23 (4825 hom., cov: 32)
• Consequence: ST18 NM_001352837.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ST18	NM_001352837.2	c.55+1029T>G		intron_variant		ENST00000689386.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ST18	ENST00000689386.1	c.55+1029T>G		intron_variant			NM_001352837.2	P1

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35043 AN: 151956 Hom.: 4810 Cov.: 32

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.231 AC: 35101 AN: 152074 Hom.: 4825 Cov.: 32 AF XY: 0.228 AC XY: 16982 AN XY: 74336

Gnomad4 AFR AF: 0.380

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.222

Alfa AF: 0.212 Hom.: 466

Bravo AF: 0.240

Asia WGS AF: 0.148 AC: 515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.94
Dann	Benign	0.42

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: rs2360806; hg19: chr8-53125734;