rs4891159

Positions:

• chr18-76389985-G-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF516	NM_014643.4	c.1811-9682C>T		intron_variant		ENST00000443185.7	NP_055458.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF516	ENST00000443185.7	c.1811-9682C>T		intron_variant		1	NM_014643.4	ENSP00000394757	P1

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

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.365

Gnomad4 ASJ AF: 0.440

Gnomad4 EAS AF: 0.480

Gnomad4 SAS AF: 0.337

Gnomad4 FIN AF: 0.368

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.368

Alfa AF: 0.407 Hom.: 12358

Bravo AF: 0.348

Asia WGS AF: 0.364 AC: 1263 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	2.1
DANN	Benign	0.59
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs4891159; hg19: chr18-74101941;