8-52301705-C-T

Variant names:

• chr8-52301705-C-T
• rs7009219
• NM_001352837.2:c.-464-71628G>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.-464-71628G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,140 control chromosomes in the GnomAD database, including 1,935 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 0.12 (1935 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: ST18 NM_001352837.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.705
• 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]

ENSG00000253924 (HGNC:58430):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ST18	NM_001352837.2	c.-464-71628G>A		intron_variant	Intron 2 of 25	ENST00000689386.1	NP_001339766.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ST18	ENST00000689386.1	c.-464-71628G>A		intron_variant	Intron 2 of 25		NM_001352837.2	ENSP00000509475.1

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18746 AN: 152022 Hom.: 1923 Cov.: 33

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.0634

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.0444

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0464

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.123 AC: 18788 AN: 152140 Hom.: 1935 Cov.: 33 AF XY: 0.124 AC XY: 9189 AN XY: 74392

African (AFR) AF: 0.261 AC: 10828 AN: 41480

American (AMR) AF: 0.102 AC: 1558 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0634 AC: 220 AN: 3468

East Asian (EAS) AF: 0.320 AC: 1654 AN: 5168

South Asian (SAS) AF: 0.133 AC: 642 AN: 4818

European-Finnish (FIN) AF: 0.0444 AC: 470 AN: 10588

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0464 AC: 3159 AN: 68010

Other (OTH) AF: 0.106 AC: 223 AN: 2108

Alfa AF: 0.0814 Hom.: 1921

Bravo AF: 0.136

Asia WGS AF: 0.203 AC: 704 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	11
DANN	Benign	0.28
PhyloP100		0.70
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: rs7009219; hg19: chr8-53214265;