17-12019587-G-T

Variant names:

• chr17-12019587-G-T
• rs3826392
• XM_024450911.2:c.-329+1736C>A

Variant summary

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

The ENST00000579522.1(ENSG00000293152):​n.186+1736C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.662 in 151,690 control chromosomes in the GnomAD database, including 34,748 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 0.66 (34748 hom., cov: 29)
• Consequence: ENSG00000293152 ENST00000579522.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.523
• Publications: 24 publications found

Genes affected

ZNF18 (HGNC:12969): (zinc finger protein 18) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000293152 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.796 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000579522.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293152	ENST00000578024.1	TSL:4	n.24+1736C>A		intron	N/A
	ENSG00000293152	ENST00000579522.1	TSL:3	n.186+1736C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.662 AC: 100356 AN: 151572 Hom.: 34738 Cov.: 29

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.635

Gnomad AMR AF: 0.714

Gnomad ASJ AF: 0.792

Gnomad EAS AF: 0.812

Gnomad SAS AF: 0.818

Gnomad FIN AF: 0.728

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.746

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.662 AC: 100408 AN: 151690 Hom.: 34748 Cov.: 29 AF XY: 0.668 AC XY: 49448 AN XY: 74074

African (AFR) AF: 0.439 AC: 18140 AN: 41288

American (AMR) AF: 0.714 AC: 10880 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.792 AC: 2748 AN: 3468

East Asian (EAS) AF: 0.812 AC: 4164 AN: 5126

South Asian (SAS) AF: 0.818 AC: 3929 AN: 4806

European-Finnish (FIN) AF: 0.728 AC: 7662 AN: 10522

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.746 AC: 50645 AN: 67928

Other (OTH) AF: 0.688 AC: 1447 AN: 2104

Alfa AF: 0.712 Hom.: 51987

Bravo AF: 0.647

Asia WGS AF: 0.795 AC: 2765 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.53
DANN	Benign	0.68
PhyloP100		-0.52

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3826392;

hg19: chr17-11922904;