7-64978289-G-C

Variant names:

• chr7-64978289-G-C
• rs1404453
• ENST00000282869.11:c.1282C>G

Variant summary

Our verdict is Uncertain significance. Variant got 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. 13/20 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

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

Verdict is Uncertain_significance. Variant got 0 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ERV3-1-ZNF117	NM_001348050.2	c.1282C>G	p.Arg428Gly	missense_variant	Exon 4 of 4		NP_001334979.1
ZNF117	NM_015852.5	c.1282C>G	p.Arg428Gly	missense_variant	Exon 4 of 4		NP_056936.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF117	ENST00000282869.11	c.1282C>G	p.Arg428Gly	missense_variant	Exon 4 of 4	1		ENSP00000282869.5
ZNF117	ENST00000620222.4	c.1282C>G	p.Arg428Gly	missense_variant	Exon 3 of 3	1

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Cov.: 75

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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;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;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.4	L;L
PROVEAN	Uncertain	-3.5	D;.
REVEL	Benign	0.042
Sift	Benign	0.30	T;.
Sift4G	Benign	0.16	T;T
Polyphen		0.81	P;P
Vest4		0.12
MutPred		0.62		Loss of MoRF binding (P = 0.0143);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

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: rs1404453; hg19: chr7-64438667;