17-11981199-C-T

Variant names:

• chr17-11981199-C-T
• rs10852800
• NM_001303281.2:c.862+2098G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001303281.2. 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
	ZNF18	NM_001303281.2	MANE Select	c.862+2098G>A		intron	N/A	NP_001290210.1	P17022-1
	ZNF18	NM_144680.4		c.862+2098G>A		intron	N/A	NP_653281.2	P17022-1
	ZNF18	NM_001303282.2		c.859+2098G>A		intron	N/A	NP_001290211.1	P17022-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF18	ENST00000580306.7	TSL:2 MANE Select	c.862+2098G>A		intron	N/A	ENSP00000463471.1	P17022-1
	ZNF18	ENST00000580613.5	TSL:1	c.862+2098G>A		intron	N/A	ENSP00000462296.3	P17022-1
	ZNF18	ENST00000454073.7	TSL:1	c.859+2098G>A		intron	N/A	ENSP00000391376.3	P17022-2

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

African (AFR) AF: 0.126 AC: 5219 AN: 41490

American (AMR) AF: 0.213 AC: 3256 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 573 AN: 3466

East Asian (EAS) AF: 0.193 AC: 997 AN: 5178

South Asian (SAS) AF: 0.144 AC: 692 AN: 4822

European-Finnish (FIN) AF: 0.209 AC: 2207 AN: 10578

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12660 AN: 67988

Other (OTH) AF: 0.179 AC: 379 AN: 2112

Alfa AF: 0.179 Hom.: 4230

Bravo AF: 0.176

Asia WGS AF: 0.156 AC: 541 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.63
PhyloP100		-0.0010
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: rs10852800; hg19: chr17-11884516;