7-127386117-G-T
Position:
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_176814.5(ZNF800):c.100C>A(p.Gln34Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000548 in 1,459,414 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000055 ( 0 hom. )
Consequence
ZNF800
NM_176814.5 missense
NM_176814.5 missense
Scores
1
5
11
Clinical Significance
Conservation
PhyloP100: 9.27
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.24815676).
BS2
High AC in GnomAdExome4 at 8 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF800 | NM_176814.5 | c.100C>A | p.Gln34Lys | missense_variant | 3/6 | ENST00000265827.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF800 | ENST00000265827.8 | c.100C>A | p.Gln34Lys | missense_variant | 3/6 | 1 | NM_176814.5 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
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32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250702Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135528
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GnomAD4 exome AF: 0.00000548 AC: 8AN: 1459414Hom.: 0 Cov.: 29 AF XY: 0.00000826 AC XY: 6AN XY: 726018
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GnomAD4 genome Cov.: 32
GnomAD4 genome
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32
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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 submitter | clinical testing | Ambry Genetics | Jun 02, 2023 | The c.100C>A (p.Q34K) alteration is located in exon 3 (coding exon 2) of the ZNF800 gene. This alteration results from a C to A substitution at nucleotide position 100, causing the glutamine (Q) at amino acid position 34 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;T;T;T;T;T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;L;L;.;.;.;.
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N;.;N;N;N
REVEL
Benign
Sift
Benign
T;T;T;.;T;T;T
Sift4G
Benign
T;T;T;T;T;T;.
Polyphen
D;D;D;.;.;.;.
Vest4
MutPred
Gain of methylation at Q34 (P = 0.0056);Gain of methylation at Q34 (P = 0.0056);Gain of methylation at Q34 (P = 0.0056);Gain of methylation at Q34 (P = 0.0056);Gain of methylation at Q34 (P = 0.0056);Gain of methylation at Q34 (P = 0.0056);Gain of methylation at Q34 (P = 0.0056);
MVP
MPC
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at