rs4979327

Positions:

• chr9-114019036-G-A
• chr9-114019036-G-C
• chr9-114019036-G-T

Variant summary

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

The NM_001318042.2(ZNF618):​c.844+2252G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 152,080 control chromosomes in the GnomAD database, including 7,740 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 0.28 (7740 hom., cov: 33)
• Consequence: ZNF618 NM_001318042.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

Genes affected

ZNF618 (HGNC:29416): (zinc finger protein 618) Enables identical protein binding activity and transcription coregulator binding activity. Involved in positive regulation of chromatin binding activity. Located in chromatin. Part of pericentric heterochromatin. [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 (EAS) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF618	NM_001318042.2	c.844+2252G>A		intron_variant		ENST00000374126.10	NP_001304971.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF618	ENST00000374126.10	c.844+2252G>A		intron_variant		1	NM_001318042.2	ENSP00000363241	P4

Frequencies

GnomAD3 genomes AF: 0.283 AC: 43081 AN: 151962 Hom.: 7744 Cov.: 33

Gnomad AFR AF: 0.0837

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.283 AC: 43075 AN: 152080 Hom.: 7740 Cov.: 33 AF XY: 0.290 AC XY: 21567 AN XY: 74290

Gnomad4 AFR AF: 0.0835

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.228

Gnomad4 EAS AF: 0.603

Gnomad4 SAS AF: 0.309

Gnomad4 FIN AF: 0.511

Gnomad4 NFE AF: 0.346

Gnomad4 OTH AF: 0.247

Alfa AF: 0.321 Hom.: 1470

Bravo AF: 0.259

Asia WGS AF: 0.394 AC: 1372 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.18
DANN	Benign	0.21

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: rs4979327; hg19: chr9-116781316;