Genetic Variant ZNF117:c.35-126A>G (chr7-64979662-T-C) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000282869.11(ZNF117):c.35-126A>G variant causes a intron 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 33)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

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:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.99).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ERV3-1-ZNF117	NM_001348050.2 link	c.35-126A>G		intron_variant	Intron 3 of 3		NP_001334979.1
ZNF117	NM_015852.5 link	c.35-126A>G		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>G	intron_variant	Intron 3 of 3	1	ENSP00000282869.5	Q03924
ZNF117	ENST00000714026.1 link	c.35-126A>G	intron_variant	Intron 3 of 3		ENSP00000519316.1
ZNF117	ENST00000714027.1 link	c.35-126A>G	intron_variant	Intron 4 of 4		ENSP00000519317.1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

509116

Hom.:

AF XY:

0.00

AC XY:

AN XY:

254036

African (AFR)

AF:

0.00

AC:

AN:

11650

American (AMR)

AF:

0.00

AC:

AN:

11384

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

11450

East Asian (EAS)

AF:

0.00

AC:

AN:

26340

South Asian (SAS)

AF:

0.00

AC:

AN:

16046

European-Finnish (FIN)

AF:

0.00

AC:

AN:

27128

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1914

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

377872

Other (OTH)

AF:

0.00

AC:

AN:

25332

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.090

(source)

DANN

Benign

0.41

PhyloP100

-3.7

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over