chr19-30444952-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_014717.3(ZNF536):c.1390G>A(p.Glu464Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000738 in 1,611,772 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00048 ( 1 hom., cov: 33)
Exomes 𝑓: 0.000032 ( 0 hom. )
Consequence
ZNF536
NM_014717.3 missense
NM_014717.3 missense
Scores
1
6
8
Clinical Significance
Conservation
PhyloP100: 9.96
Genes affected
ZNF536 (HGNC:29025): (zinc finger protein 536) The protein encoded by this gene is a highly conserved zinc finger protein. The encoded protein is most abundant in brain, where it negatively regulates neuronal differentiation. [provided by RefSeq, Sep 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.008452743).
BP6
?
Variant 19-30444952-G-A is Benign according to our data. Variant chr19-30444952-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 760734.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd at 74 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF536 | NM_014717.3 | c.1390G>A | p.Glu464Lys | missense_variant | 2/5 | ENST00000355537.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF536 | ENST00000355537.4 | c.1390G>A | p.Glu464Lys | missense_variant | 2/5 | 1 | NM_014717.3 |
Frequencies
GnomAD3 genomes ? AF: 0.000486 AC: 74AN: 152224Hom.: 1 Cov.: 33
GnomAD3 genomes
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GnomAD3 exomes AF: 0.000169 AC: 42AN: 248262Hom.: 1 AF XY: 0.000119 AC XY: 16AN XY: 134630
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GnomAD4 exome AF: 0.0000315 AC: 46AN: 1459430Hom.: 0 Cov.: 33 AF XY: 0.0000289 AC XY: 21AN XY: 725872
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GnomAD4 genome ? AF: 0.000479 AC: 73AN: 152342Hom.: 1 Cov.: 33 AF XY: 0.000416 AC XY: 31AN XY: 74498
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 13, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Uncertain
DEOGEN2
Benign
T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationTaster
Benign
D
PrimateAI
Uncertain
T
Sift4G
Benign
T;T
Polyphen
0.88
.;P
Vest4
0.75
MVP
MPC
2.0
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at