rs2360808

Variant names:

• chr8-52213340-C-T
• rs2360808
• NM_001352837.2:c.55+863G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 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=-0.81).
• 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 rank	MANE	Protein	UniProt
ST18	NM_001352837.2	c.55+863G>A		intron_variant	Intron 7 of 25	ENST00000689386.1	NP_001339766.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ST18	ENST00000689386.1	c.55+863G>A		intron_variant	Intron 7 of 25		NM_001352837.2	ENSP00000509475.1

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

African (AFR) AF: 0.355 AC: 14656 AN: 41324

American (AMR) AF: 0.114 AC: 1734 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.0288 AC: 100 AN: 3470

East Asian (EAS) AF: 0.102 AC: 524 AN: 5158

South Asian (SAS) AF: 0.0476 AC: 228 AN: 4788

European-Finnish (FIN) AF: 0.0570 AC: 600 AN: 10528

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0163 AC: 1111 AN: 67974

Other (OTH) AF: 0.109 AC: 229 AN: 2092

Alfa AF: 0.0517 Hom.: 3308

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
PhyloP100		-4.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2360808; hg19: chr8-53125900;