chr9-114018185-G-A

Variant names:

• chr9-114018185-G-A
• rs4979326
• NM_001318042.2:c.844+1401G>A

Variant summary

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

The NM_001318042.2(ZNF618):​c.844+1401G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 152,144 control chromosomes in the GnomAD database, including 7,843 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 0.29 (7843 hom., cov: 33)
• Consequence: ZNF618 NM_001318042.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.215
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001318042.2. 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
	ZNF618	NM_001318042.2	MANE Select	c.844+1401G>A		intron	N/A	NP_001304971.1
	ZNF618	NM_001318041.2		c.748+1401G>A		intron	N/A	NP_001304970.1
	ZNF618	NM_001318040.2		c.748+1401G>A		intron	N/A	NP_001304969.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF618	ENST00000374126.10	TSL:1 MANE Select	c.844+1401G>A		intron	N/A	ENSP00000363241.5
	ZNF618	ENST00000615615.4	TSL:1	c.748+1401G>A		intron	N/A	ENSP00000483198.1
	ZNF618	ENST00000968409.1		c.904+1401G>A		intron	N/A	ENSP00000638468.1

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43990 AN: 152026 Hom.: 7848 Cov.: 33

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.289 AC: 43986 AN: 152144 Hom.: 7843 Cov.: 33 AF XY: 0.296 AC XY: 22051 AN XY: 74372

African (AFR) AF: 0.103 AC: 4277 AN: 41512

American (AMR) AF: 0.296 AC: 4529 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.228 AC: 790 AN: 3470

East Asian (EAS) AF: 0.602 AC: 3102 AN: 5152

South Asian (SAS) AF: 0.320 AC: 1543 AN: 4822

European-Finnish (FIN) AF: 0.510 AC: 5402 AN: 10582

Middle Eastern (MID) AF: 0.147 AC: 43 AN: 292

European-Non Finnish (NFE) AF: 0.346 AC: 23497 AN: 67992

Other (OTH) AF: 0.250 AC: 528 AN: 2112

Alfa AF: 0.307 Hom.: 22377

Bravo AF: 0.265

Asia WGS AF: 0.400 AC: 1392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.46
PhyloP100		0.21
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: rs4979326; hg19: chr9-116780465;