9-113978212-G-A

Variant names:

• chr9-113978212-G-A
• rs9332459
• NM_001318042.2:c.77+9052G>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.77+9052G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 152,140 control chromosomes in the GnomAD database, including 23,802 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 0.56 (23802 hom., cov: 33)
• Consequence: ZNF618 NM_001318042.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.595
• Publications: 6 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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF618	NM_001318042.2	c.77+9052G>A		intron_variant	Intron 2 of 14	ENST00000374126.10	NP_001304971.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF618	ENST00000374126.10	c.77+9052G>A		intron_variant	Intron 2 of 14	1	NM_001318042.2	ENSP00000363241.5

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84411 AN: 152022 Hom.: 23797 Cov.: 33

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.691

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.628

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.555 AC: 84451 AN: 152140 Hom.: 23802 Cov.: 33 AF XY: 0.554 AC XY: 41184 AN XY: 74374

African (AFR) AF: 0.497 AC: 20618 AN: 41504

American (AMR) AF: 0.600 AC: 9181 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.646 AC: 2243 AN: 3470

East Asian (EAS) AF: 0.341 AC: 1765 AN: 5174

South Asian (SAS) AF: 0.629 AC: 3027 AN: 4814

European-Finnish (FIN) AF: 0.503 AC: 5318 AN: 10572

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.591 AC: 40151 AN: 67992

Other (OTH) AF: 0.612 AC: 1293 AN: 2112

Alfa AF: 0.585 Hom.: 14385

Bravo AF: 0.558

Asia WGS AF: 0.520 AC: 1809 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.5
DANN	Benign	0.50
PhyloP100		0.59
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: rs9332459; hg19: chr9-116740492;