chr9-114004415-G-A

Position:

• chr9-114004415-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001318042.2(ZNF618):​c.550+1753G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 152,058 control chromosomes in the GnomAD database, including 8,674 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 0.32 (8674 hom., cov: 32)
• Consequence: ZNF618 NM_001318042.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.825

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF618	NM_001318042.2	c.550+1753G>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.550+1753G>A		intron_variant		1	NM_001318042.2	ENSP00000363241	P4

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48549 AN: 151942 Hom.: 8675 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.319 AC: 48566 AN: 152058 Hom.: 8674 Cov.: 32 AF XY: 0.325 AC XY: 24143 AN XY: 74306

Gnomad4 AFR AF: 0.189

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.605

Gnomad4 SAS AF: 0.327

Gnomad4 FIN AF: 0.512

Gnomad4 NFE AF: 0.353

Gnomad4 OTH AF: 0.277

Alfa AF: 0.329 Hom.: 8151

Bravo AF: 0.300

Asia WGS AF: 0.417 AC: 1449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	18
DANN	Benign	0.70

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: rs7858120; hg19: chr9-116766695;