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 ENST00000282869.11(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
ENST00000282869.11 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ERV3-1-ZNF117	NM_001348050.2 link	c.35-126A>C		intron_variant	Intron 3 of 3		NP_001334979.1
ZNF117	NM_015852.5 link	c.35-126A>C		intron_variant	Intron 3 of 3		NP_056936.2	Q03924

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein	UniProt
ZNF117	ENST00000282869.11 link	c.35-126A>C	intron_variant	Intron 3 of 3	1	ENSP00000282869.5	Q03924
ZNF117	ENST00000714026.1 link	c.35-126A>C	intron_variant	Intron 3 of 3		ENSP00000519316.1
ZNF117	ENST00000714027.1 link	c.35-126A>C	intron_variant	Intron 4 of 4		ENSP00000519317.1

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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over