7-64978289-G-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_015852.5(ZNF117):​c.1282C>T​(p.Arg428*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.939 in 1,612,614 control chromosomes in the GnomAD database, including 713,237 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 0.90 (61559 hom., cov: 30)
  • Exomes 𝑓: 0.94 (651678 hom.)
• Consequence: ZNF117 NM_015852.5 stop_gained
• 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: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.947 is higher than 0.05.

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>T	p.Arg428*	stop_gained	Exon 4 of 4	NP_056936.2
	ERV3-1-ZNF117	NM_001348050.2		c.1282C>T	p.Arg428*	stop_gained	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>T	p.Arg428*	stop_gained	Exon 4 of 4	ENSP00000282869.5
	ZNF117	ENST00000714026.1		c.1282C>T	p.Arg428*	stop_gained	Exon 4 of 4	ENSP00000519316.1
	ZNF117	ENST00000714027.1		c.1282C>T	p.Arg428*	stop_gained	Exon 5 of 5	ENSP00000519317.1

Frequencies

GnomAD3 genomes AF: 0.898 AC: 135961 AN: 151468 Hom.: 61530 Cov.: 30

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.990

Gnomad AMR AF: 0.932

Gnomad ASJ AF: 0.975

Gnomad EAS AF: 0.848

Gnomad SAS AF: 0.968

Gnomad FIN AF: 0.958

Gnomad MID AF: 0.948

Gnomad NFE AF: 0.953

Gnomad OTH AF: 0.917

GnomAD2 exomes AF: 0.934 AC: 232276 AN: 248572 AF XY: 0.939

Gnomad AFR exome AF: 0.765

Gnomad AMR exome AF: 0.934

Gnomad ASJ exome AF: 0.977

Gnomad EAS exome AF: 0.850

Gnomad FIN exome AF: 0.954

Gnomad NFE exome AF: 0.954

Gnomad OTH exome AF: 0.946

GnomAD4 exome AF: 0.944 AC: 1378850 AN: 1461026 Hom.: 651678 Cov.: 75 AF XY: 0.945 AC XY: 687191 AN XY: 726840

African (AFR) AF: 0.763 AC: 25520 AN: 33432

American (AMR) AF: 0.933 AC: 41634 AN: 44624

Ashkenazi Jewish (ASJ) AF: 0.976 AC: 25476 AN: 26106

East Asian (EAS) AF: 0.852 AC: 33802 AN: 39660

South Asian (SAS) AF: 0.969 AC: 83586 AN: 86232

European-Finnish (FIN) AF: 0.952 AC: 50675 AN: 53240

Middle Eastern (MID) AF: 0.954 AC: 5502 AN: 5766

European-Non Finnish (NFE) AF: 0.950 AC: 1056070 AN: 1111594

Other (OTH) AF: 0.937 AC: 56585 AN: 60372

GnomAD4 genome AF: 0.897 AC: 136042 AN: 151588 Hom.: 61559 Cov.: 30 AF XY: 0.898 AC XY: 66578 AN XY: 74126

African (AFR) AF: 0.766 AC: 31668 AN: 41328

American (AMR) AF: 0.932 AC: 14201 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.975 AC: 3366 AN: 3452

East Asian (EAS) AF: 0.849 AC: 4358 AN: 5136

South Asian (SAS) AF: 0.968 AC: 4655 AN: 4808

European-Finnish (FIN) AF: 0.958 AC: 10145 AN: 10586

Middle Eastern (MID) AF: 0.941 AC: 273 AN: 290

European-Non Finnish (NFE) AF: 0.953 AC: 64551 AN: 67746

Other (OTH) AF: 0.916 AC: 1922 AN: 2098

Alfa AF: 0.941 Hom.: 21115

Bravo AF: 0.889

TwinsUK AF: 0.950 AC: 3522

ALSPAC AF: 0.940 AC: 3624

ESP6500AA AF: 0.783 AC: 3292

ESP6500EA AF: 0.955 AC: 8119

ExAC AF: 0.931 AC: 112710

Asia WGS AF: 0.905 AC: 3146 AN: 3478

EpiCase AF: 0.957

EpiControl AF: 0.957

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.27	T
BayesDel_noAF	Uncertain	-0.020
CADD	Benign	22
DANN	Benign	0.88
Eigen	Benign	-0.82
Eigen_PC	Benign	-1.3
FATHMM_MKL	Benign	0.00026	N
PhyloP100		-2.9
Vest4		0.041
GERP RS		-2.2
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=188/12	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; COSMIC: COSV107296982; COSMIC: COSV107296982;