7-64978289-G-C

Variant names:

• chr7-64978289-G-C
• rs1404453
• NM_015852.5:c.1282C>G

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_015852.5(ZNF117):​c.1282C>G​(p.Arg428Gly) variant causes a missense 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. 14/21 in silico tools predict 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: 30)
• Consequence: ZNF117 NM_015852.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.90
• Publications: 35 publications found

Genes affected

ZNF117 (HGNC:12897): (zinc finger protein 117) This gene encodes a protein containing multiple C2H2-type zinc finger motifs. Readthrough transcription occurs between this gene and the upstream endogenous retrovirus group 3 member 1 (ERV3-1) locus, and may result in additional transcript variants encoding the zinc finger protein. [provided by RefSeq, Jan 2017]

ERV3-1-ZNF117 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.13074547).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015852.5. 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
	ZNF117	NM_015852.5	MANE Select	c.1282C>G	p.Arg428Gly	missense	Exon 4 of 4	NP_056936.2
	ERV3-1-ZNF117	NM_001348050.2		c.1282C>G	p.Arg428Gly	missense	Exon 4 of 4	NP_001334979.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF117	ENST00000282869.11	TSL:1 MANE Select	c.1282C>G	p.Arg428Gly	missense	Exon 4 of 4	ENSP00000282869.5
	ZNF117	ENST00000714026.1		c.1282C>G	p.Arg428Gly	missense	Exon 4 of 4	ENSP00000519316.1
	ZNF117	ENST00000714027.1		c.1282C>G	p.Arg428Gly	missense	Exon 5 of 5	ENSP00000519317.1

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Cov.: 75

GnomAD4 genome Cov.: 30

Alfa AF: 0.00 Hom.: 21115

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.23
BayesDel_addAF	Benign	-0.33	T
BayesDel_noAF	Benign	-0.72
CADD	Benign	1.8
DANN	Benign	0.54
DEOGEN2	Benign	0.028	T
Eigen	Benign	-1.4
Eigen_PC	Benign	-1.6
FATHMM_MKL	Benign	0.00024	N
LIST_S2	Benign	0.061	T
M_CAP	Benign	0.00061	T
MetaRNN	Benign	0.13	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.4	L
PhyloP100		-2.9
PROVEAN	Uncertain	-3.5	D
REVEL	Benign	0.042
Sift	Benign	0.30	T
Sift4G	Benign	0.16	T
Polyphen		0.81	P
Vest4		0.12
MutPred		0.62		Loss of MoRF binding (P = 0.0143)
MVP		0.14
MPC		0.015
ClinPred		0.28	T
GERP RS		-2.2
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.10
gMVP		0.017
Mutation Taster		=100/0	polymorphism

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: rs1404453; hg19: chr7-64438667;