rs4979321

Variant names:

• chr9-114007235-C-G
• rs4979321
• NM_001318042.2:c.551-115C>G

Your query was ambiguous. Multiple possible variants found:

• chr9-114007235-C-G
• chr9-114007235-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001318042.2(ZNF618):​c.551-115C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: ZNF618 NM_001318042.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.27
• Publications: 5 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF618	NM_001318042.2	MANE Select	c.551-115C>G		intron	N/A	NP_001304971.1
	ZNF618	NM_001318041.2		c.455-115C>G		intron	N/A	NP_001304970.1
	ZNF618	NM_001318040.2		c.455-115C>G		intron	N/A	NP_001304969.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF618	ENST00000374126.10	TSL:1 MANE Select	c.551-115C>G		intron	N/A	ENSP00000363241.5
	ZNF618	ENST00000615615.4	TSL:1	c.455-115C>G		intron	N/A	ENSP00000483198.1
	ZNF618	ENST00000288466.11	TSL:2	c.455-115C>G		intron	N/A	ENSP00000288466.7

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.099
DANN	Benign	0.86
PhyloP100		-2.3

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: rs4979321; hg19: chr9-116769515;