chr19-56384842-A-C

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_001320371.4(ZNF582):​c.575T>G​(p.Ile192Ser) variant causes a missense 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. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)

Consequence

ZNF582
NM_001320371.4 missense

Scores

4
15

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.25
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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.35969543).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ZNF582NM_001320371.4 linkuse as main transcriptc.575T>G p.Ile192Ser missense_variant 5/5 ENST00000586929.6 NP_001307300.2
ZNF582NM_144690.3 linkuse as main transcriptc.575T>G p.Ile192Ser missense_variant 5/5 NP_653291.1
ZNF582XR_007066621.1 linkuse as main transcriptn.748T>G non_coding_transcript_exon_variant 5/6
ZNF582XR_430188.4 linkuse as main transcriptn.970T>G non_coding_transcript_exon_variant 5/6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ZNF582ENST00000586929.6 linkuse as main transcriptc.575T>G p.Ile192Ser missense_variant 5/51 NM_001320371.4 ENSP00000465619 P1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
33
GnomAD4 genome
Cov.:
33

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsJan 03, 2024The c.575T>G (p.I192S) alteration is located in exon 5 (coding exon 4) of the ZNF582 gene. This alteration results from a T to G substitution at nucleotide position 575, causing the isoleucine (I) at amino acid position 192 to be replaced by a serine (S). 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
Benign
0.17
BayesDel_addAF
Benign
-0.10
T
BayesDel_noAF
Benign
-0.38
CADD
Benign
22
DANN
Uncertain
0.99
DEOGEN2
Benign
0.23
T;T;T
Eigen
Benign
-0.49
Eigen_PC
Benign
-0.56
FATHMM_MKL
Benign
0.58
D
LIST_S2
Benign
0.39
.;T;.
M_CAP
Benign
0.016
T
MetaRNN
Benign
0.36
T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.79
N;N;N
MutationTaster
Benign
1.0
N;N
PrimateAI
Benign
0.45
T
PROVEAN
Uncertain
-4.3
D;.;.
REVEL
Benign
0.19
Sift
Uncertain
0.012
D;.;.
Sift4G
Uncertain
0.024
D;D;D
Polyphen
0.82
P;P;P
Vest4
0.50
MutPred
0.66
Gain of disorder (P = 0.0108);Gain of disorder (P = 0.0108);Gain of disorder (P = 0.0108);
MVP
0.14
MPC
0.22
ClinPred
0.38
T
GERP RS
3.8
Varity_R
0.36
gMVP
0.19

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr19-56896211; API