18-76389985-G-A

Variant names:

• chr18-76389985-G-A
• rs4891159
• NM_014643.4:c.1811-9682C>T

Variant summary

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

The NM_014643.4(ZNF516):​c.1811-9682C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 152,054 control chromosomes in the GnomAD database, including 9,908 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 0.35 (9908 hom., cov: 32)
• Consequence: ZNF516 NM_014643.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.362
• Publications: 11 publications found

Genes affected

ZNF516 (HGNC:28990): (zinc finger protein 516) Zinc-finger proteins bind nucleic acids and play important roles in various cellular functions, including cell proliferation, differentiation, and apoptosis. This gene encodes a zinc-finger protein, and belongs to the krueppel C2H2-type zinc-finger protein family. It may be involved in transcriptional regulation. [provided by RefSeq, Sep 2012]

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 (EAS) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014643.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF516	NM_014643.4	MANE Select	c.1811-9682C>T		intron	N/A	NP_055458.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF516	ENST00000443185.7	TSL:1 MANE Select	c.1811-9682C>T		intron	N/A	ENSP00000394757.2

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53166 AN: 151936 Hom.: 9908 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.350 AC: 53166 AN: 152054 Hom.: 9908 Cov.: 32 AF XY: 0.348 AC XY: 25873 AN XY: 74320

African (AFR) AF: 0.218 AC: 9058 AN: 41488

American (AMR) AF: 0.365 AC: 5578 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 1528 AN: 3470

East Asian (EAS) AF: 0.480 AC: 2480 AN: 5170

South Asian (SAS) AF: 0.337 AC: 1619 AN: 4810

European-Finnish (FIN) AF: 0.368 AC: 3883 AN: 10564

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.410 AC: 27855 AN: 67964

Other (OTH) AF: 0.368 AC: 778 AN: 2112

Alfa AF: 0.394 Hom.: 35741

Bravo AF: 0.348

Asia WGS AF: 0.364 AC: 1263 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	2.1
DANN	Benign	0.59
PhyloP100		0.36
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs4891159; hg19: chr18-74101941;