17-11981199-C-T

Position:

• chr17-11981199-C-T

Variant summary

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

The NM_001303281.2(ZNF18):​c.862+2098G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 152,110 control chromosomes in the GnomAD database, including 2,405 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 0.17 (2405 hom., cov: 32)
• Consequence: ZNF18 NM_001303281.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00100

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]

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 (AMR) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF18	NM_001303281.2	c.862+2098G>A		intron_variant		ENST00000580306.7	NP_001290210.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF18	ENST00000580306.7	c.862+2098G>A		intron_variant		2	NM_001303281.2	ENSP00000463471.1

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26302 AN: 151992 Hom.: 2400 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.173 AC: 26326 AN: 152110 Hom.: 2405 Cov.: 32 AF XY: 0.173 AC XY: 12876 AN XY: 74354

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.213

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.193

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.209

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.179

Alfa AF: 0.179 Hom.: 3329

Bravo AF: 0.176

Asia WGS AF: 0.156 AC: 541 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.63

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: rs10852800; hg19: chr17-11884516;