9-113980202-A-G

Variant names:

• chr9-113980202-A-G
• rs1408112
• NM_001318042.2:c.78-8119A>G

Variant summary

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

The NM_001318042.2(ZNF618):​c.78-8119A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.567 in 151,932 control chromosomes in the GnomAD database, including 24,710 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 0.57 (24710 hom., cov: 32)
• Consequence: ZNF618 NM_001318042.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07
• Publications: 1 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=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.614 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF618	NM_001318042.2	c.78-8119A>G		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.78-8119A>G		intron_variant	Intron 2 of 14	1	NM_001318042.2	ENSP00000363241.5

Frequencies

GnomAD3 genomes AF: 0.567 AC: 86104 AN: 151812 Hom.: 24703 Cov.: 32

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.692

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.653

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.614

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

GnomAD4 genome AF: 0.567 AC: 86149 AN: 151932 Hom.: 24710 Cov.: 32 AF XY: 0.565 AC XY: 41943 AN XY: 74232

African (AFR) AF: 0.529 AC: 21904 AN: 41430

American (AMR) AF: 0.607 AC: 9267 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.653 AC: 2265 AN: 3468

East Asian (EAS) AF: 0.350 AC: 1801 AN: 5146

South Asian (SAS) AF: 0.632 AC: 3043 AN: 4812

European-Finnish (FIN) AF: 0.504 AC: 5308 AN: 10530

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

European-Non Finnish (NFE) AF: 0.595 AC: 40403 AN: 67960

Other (OTH) AF: 0.617 AC: 1301 AN: 2110

Alfa AF: 0.562 Hom.: 2987

Bravo AF: 0.571

Asia WGS AF: 0.532 AC: 1852 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.27
DANN	Benign	0.74
PhyloP100		-2.1
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: rs1408112; hg19: chr9-116742482;