7-64979662-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015852.5(ZNF117):c.35-126A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.984 in 661,166 control chromosomes in the GnomAD database, including 320,764 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 0.95 (68900 hom., cov: 33)
  • Exomes 𝑓: 0.99 (251864 hom.)
• Consequence: ZNF117 NM_015852.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.66

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF117	NM_015852.5	c.35-126A>C		intron_variant		ENST00000282869.11
ERV3-1-ZNF117	NM_001348050.2	c.35-126A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF117	ENST00000282869.11	c.35-126A>C		intron_variant		1	NM_015852.5	P1
ZNF117	ENST00000620222.4	c.35-126A>C		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.949 AC: 144181 AN: 151960 Hom.: 68873 Cov.: 33

Gnomad AFR AF: 0.824

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.977

Gnomad ASJ AF: 0.995

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.998

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.984

Gnomad NFE AF: 0.999

Gnomad OTH AF: 0.970

GnomAD4 exome AF: 0.994 AC: 506180 AN: 509088 Hom.: 251864 AF XY: 0.995 AC XY: 252733 AN XY: 254020

Gnomad4 AFR exome AF: 0.824

Gnomad4 AMR exome AF: 0.983

Gnomad4 ASJ exome AF: 0.996

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.998

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.999

Gnomad4 OTH exome AF: 0.984

GnomAD4 genome AF: 0.949 AC: 144260 AN: 152078 Hom.: 68900 Cov.: 33 AF XY: 0.950 AC XY: 70610 AN XY: 74364

Gnomad4 AFR AF: 0.824

Gnomad4 AMR AF: 0.977

Gnomad4 ASJ AF: 0.995

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.998

Gnomad4 FIN AF: 1.00

Gnomad4 NFE AF: 0.999

Gnomad4 OTH AF: 0.970

Alfa AF: 0.973 Hom.: 4730

Bravo AF: 0.941

Asia WGS AF: 0.989 AC: 3440 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.085
Dann	Benign	0.40
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs1524821; hg19: chr7-64440040;