Genetic Variant ZNF582:p.Gln350Arg (chr19-56384368-T-C) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001320371.4(ZNF582):c.1049A>G(p.Gln350Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,611,136 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000026 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

ZNF582
NM_001320371.4 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.205

Variant links:

Genes affected

ZNF582 (HGNC:26421): (zinc finger protein 582) The protein encoded by this gene is a zing finger protein and putative transcription factor that is highly methylated in cervical cancers. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2016]

ZNF582 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.11308086).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF582	NM_001320371.4 link	c.1049A>G	p.Gln350Arg	missense_variant	Exon 5 of 5	ENST00000586929.6	NP_001307300.2	Q96NG8
ZNF582	NM_144690.3 link	c.1049A>G	p.Gln350Arg	missense_variant	Exon 5 of 5		NP_653291.1	Q96NG8A0A024R4P7
ZNF582	XR_007066621.1 link	n.1222A>G		non_coding_transcript_exon_variant	Exon 5 of 6
ZNF582	XR_430188.4 link	n.1444A>G		non_coding_transcript_exon_variant	Exon 5 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
ZNF582	ENST00000586929.6 link	c.1049A>G	p.Gln350Arg	missense_variant	Exon 5 of 5	1	NM_001320371.4	ENSP00000465619.1	Q96NG8
ZNF582	ENST00000301310.8 link	c.1049A>G	p.Gln350Arg	missense_variant	Exon 5 of 5	1		ENSP00000301310.3	Q96NG8
ZNF582	ENST00000589143.5 link	c.232+5633A>G		intron_variant	Intron 4 of 4	5		ENSP00000468679.1	K7ESE7
ZNF582	ENST00000589895.2 link	c.232+5633A>G		intron_variant	Intron 4 of 4	2		ENSP00000465639.1	K7EKI7

Frequencies

GnomAD3 genomes

AF:

0.0000263

AC:

AN:

152140

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000588

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.00000137

AC:

AN:

1458996

Hom.:

Cov.:

AF XY:

0.00000138

AC XY:

AN XY:

725688

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000180

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.0000263

AC:

AN:

152140

Hom.:

Cov.:

AF XY:

0.0000269

AC XY:

AN XY:

74310

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000588

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.0000712

Hom.:

Bravo

AF:

0.0000189

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Dec 13, 2023

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.1049A>G (p.Q350R) alteration is located in exon 5 (coding exon 4) of the ZNF582 gene. This alteration results from a A to G substitution at nucleotide position 1049, causing the glutamine (Q) at amino acid position 350 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.34

BayesDel_addAF

Benign

-0.23

BayesDel_noAF

Benign

-0.56

CADD

Benign

DANN

Benign

0.69

DEOGEN2

Benign

0.011

T;T;T

Eigen

Benign

-0.31

Eigen_PC

Benign

-0.41

FATHMM_MKL

Benign

0.51

LIST_S2

Benign

0.031

.;T;.

M_CAP

Benign

0.0098

MetaRNN

Benign

0.11

T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

-0.79

N;N;N

PrimateAI

Benign

0.41

PROVEAN

Benign

-1.1

N;.;.

REVEL

Benign

0.11

Sift

Benign

0.46

T;.;.

Sift4G

Benign

0.57

T;T;T

Polyphen

0.99

D;D;D

Vest4

0.099

MutPred

0.24

Gain of MoRF binding (P = 0.018);Gain of MoRF binding (P = 0.018);Gain of MoRF binding (P = 0.018);

MVP

0.20

MPC

0.59

ClinPred

0.55

GERP RS

4.7

Varity_R

0.13

gMVP

0.081

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

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over