rs7858120

Variant names:

• chr9-114004415-G-A
• rs7858120
• NM_001318042.2:c.550+1753G>A

Your query was ambiguous. Multiple possible variants found:

• chr9-114004415-G-A
• chr9-114004415-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 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 -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.

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.550+1753G>A		intron	N/A	NP_001304971.1	Q5T7W0-1
	ZNF618	NM_001318041.2		c.454+1753G>A		intron	N/A	NP_001304970.1
	ZNF618	NM_001318040.2		c.454+1753G>A		intron	N/A	NP_001304969.1	Q5T7W0-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF618	ENST00000374126.10	TSL:1 MANE Select	c.550+1753G>A		intron	N/A	ENSP00000363241.5	Q5T7W0-1
	ZNF618	ENST00000615615.4	TSL:1	c.454+1753G>A		intron	N/A	ENSP00000483198.1	Q5T7W0-4
	ZNF618	ENST00000968409.1		c.550+1753G>A		intron	N/A	ENSP00000638468.1

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

African (AFR) AF: 0.189 AC: 7850 AN: 41488

American (AMR) AF: 0.314 AC: 4801 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 871 AN: 3464

East Asian (EAS) AF: 0.605 AC: 3121 AN: 5160

South Asian (SAS) AF: 0.327 AC: 1574 AN: 4818

European-Finnish (FIN) AF: 0.512 AC: 5403 AN: 10556

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.353 AC: 24021 AN: 67956

Other (OTH) AF: 0.277 AC: 587 AN: 2116

Alfa AF: 0.324 Hom.: 10500

Bravo AF: 0.300

Asia WGS AF: 0.417 AC: 1449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	18
DANN	Benign	0.70
PhyloP100		0.82
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: rs7858120; hg19: chr9-116766695; COSMIC: COSV99930545;