Genetic Variant ZNF420:c.-124-14929T>C (chr19-37065416-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000587029.5(ZNF420):c.-124-14929T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 152,068 control chromosomes in the GnomAD database, including 21,037 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 0.52 ( 21037 hom., cov: 33)

Consequence

ZNF420
ENST00000587029.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.415

Variant links:

Genes affected

ZNF420 (HGNC:20649): (zinc finger protein 420) The protein encoded by this gene is a KRAB-type zinc finger protein that negatively-regulates p53-mediated apoptosis. Under stress conditions, the encoded protein is phosphorylated by ATM and dissociates from p53, which activates p53 and initiates apoptosis. [provided by RefSeq, Jul 2016]

ZNF420 links:

LOC105372390 (HGNC:):

LOC105372390 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein	UniProt
ZNF420	XM_011526503.3 link	c.-124-14929T>C	intron_variant	Intron 1 of 4	XP_011524805.1	Q8TAQ5-1
ZNF420	XM_047438230.1 link	c.-157-14929T>C	intron_variant	Intron 1 of 5	XP_047294186.1
ZNF420	XM_011526510.3 link	c.-121-14929T>C	intron_variant	Intron 1 of 2	XP_011524812.1
LOC105372390	XR_001754095.2 link	n.10990A>G	non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF420	ENST00000587029.5 link	c.-124-14929T>C		intron_variant	Intron 1 of 4	4		ENSP00000466057.1		K7ELF6
ZNF420	ENST00000590332.1 link	c.-78+57334T>C		intron_variant	Intron 1 of 1	4		ENSP00000468387.1		K7ERS3

Frequencies

GnomAD3 genomes

AF:

0.515

AC:

78294

AN:

151950

Hom.:

21000

Cov.:

show subpopulations

Gnomad AFR

AF:

0.621

Gnomad AMI

AF:

0.261

Gnomad AMR

AF:

0.476

Gnomad ASJ

AF:

0.453

Gnomad EAS

AF:

0.149

Gnomad SAS

AF:

0.401

Gnomad FIN

AF:

0.500

Gnomad MID

AF:

0.525

Gnomad NFE

AF:

0.505

Gnomad OTH

AF:

0.518

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.516

AC:

78403

AN:

152068

Hom.:

21037

Cov.:

AF XY:

0.510

AC XY:

37895

AN XY:

74324

show subpopulations

Gnomad4 AFR

AF:

0.621

Gnomad4 AMR

AF:

0.476

Gnomad4 ASJ

AF:

0.453

Gnomad4 EAS

AF:

0.149

Gnomad4 SAS

AF:

0.401

Gnomad4 FIN

AF:

0.500

Gnomad4 NFE

AF:

0.505

Gnomad4 OTH

AF:

0.518

Alfa

AF:

0.503

Hom.:

2981

Bravo

AF:

0.519

Asia WGS

AF:

0.336

AC:

1169

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

9.4

DANN

Benign

0.92

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over