Genetic Variant ZNF117:c.35-126A>C (chr7-64979662-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.66

Publications

1 publications found

Variant links:

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]

ZNF117 links:

ERV3-1-ZNF117 (HGNC:):

ERV3-1-ZNF117 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF117	NM_015852.5	MANE Select	c.35-126A>C		intron	N/A	NP_056936.2	Q03924
	ERV3-1-ZNF117	NM_001348050.2		c.35-126A>C		intron	N/A	NP_001334979.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ZNF117	ENST00000282869.11	TSL:1 MANE Select	c.35-126A>C	intron	N/A	ENSP00000282869.5	Q03924
ZNF117	ENST00000714026.1		c.35-126A>C	intron	N/A	ENSP00000519316.1	Q03924
ZNF117	ENST00000714027.1		c.35-126A>C	intron	N/A	ENSP00000519317.1	Q03924

Frequencies

GnomAD3 genomes

AF:

0.949

AC:

144181

AN:

151960

Hom.:

68873

Cov.:

show subpopulations

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

show subpopulations

African (AFR)

AF:

0.824

AC:

9587

AN:

11628

American (AMR)

AF:

0.983

AC:

11186

AN:

11382

Ashkenazi Jewish (ASJ)

AF:

0.996

AC:

11408

AN:

11450

East Asian (EAS)

AF:

1.00

AC:

26340

AN:

26340

South Asian (SAS)

AF:

0.998

AC:

16019

AN:

16046

European-Finnish (FIN)

AF:

1.00

AC:

27128

AN:

27128

Middle Eastern (MID)

AF:

0.992

AC:

1899

AN:

1914

European-Non Finnish (NFE)

AF:

0.999

AC:

377678

AN:

377870

Other (OTH)

AF:

0.984

AC:

24935

AN:

25330

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

118

236

353

471

589

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5742

11484

17226

22968

28710

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.949

AC:

144260

AN:

152078

Hom.:

68900

Cov.:

AF XY:

0.950

AC XY:

70610

AN XY:

74364

show subpopulations

African (AFR)

AF:

0.824

AC:

34188

AN:

41504

American (AMR)

AF:

0.977

AC:

14905

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.995

AC:

3448

AN:

3466

East Asian (EAS)

AF:

1.00

AC:

5185

AN:

5186

South Asian (SAS)

AF:

0.998

AC:

4817

AN:

4826

European-Finnish (FIN)

AF:

1.00

AC:

10610

AN:

10610

Middle Eastern (MID)

AF:

0.983

AC:

289

AN:

294

European-Non Finnish (NFE)

AF:

0.999

AC:

67855

AN:

67908

Other (OTH)

AF:

0.970

AC:

2051

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

338

676

1015

1353

1691

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

908

1816

2724

3632

4540

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.964

Hom.:

5012

Bravo

AF:

0.941

Asia WGS

AF:

0.989

AC:

3440

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.085

(source)

DANN

Benign

0.40

PhyloP100

-3.7

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over