chr18-34019364-A-G
Position:
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_003787.5(NOL4):āc.1010T>Cā(p.Ile337Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00000958 in 1,461,776 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: not found (cov: 32)
Exomes š: 0.0000096 ( 0 hom. )
Consequence
NOL4
NM_003787.5 missense
NM_003787.5 missense
Scores
5
14
Clinical Significance
Conservation
PhyloP100: 6.78
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=0.15867525).
BS2
High AC in GnomAdExome4 at 14 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NOL4 | NM_003787.5 | c.1010T>C | p.Ile337Thr | missense_variant | 6/11 | ENST00000261592.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NOL4 | ENST00000261592.10 | c.1010T>C | p.Ile337Thr | missense_variant | 6/11 | 1 | NM_003787.5 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 250806Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135562
GnomAD3 exomes
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GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461776Hom.: 0 Cov.: 32 AF XY: 0.0000124 AC XY: 9AN XY: 727192
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GnomAD4 genome Cov.: 32
GnomAD4 genome
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32
ExAC
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4
Asia WGS
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2
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3478
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 | Nov 15, 2021 | The c.1010T>C (p.I337T) alteration is located in exon 6 (coding exon 6) of the NOL4 gene. This alteration results from a T to C substitution at nucleotide position 1010, causing the isoleucine (I) at amino acid position 337 to be replaced by a threonine (T). 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
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;.;.;.;T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D;D;D;D
M_CAP
Benign
D
MetaRNN
Benign
T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.;L;.;.;.
MutationTaster
Benign
D;D;D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;.;N;.;.
REVEL
Uncertain
Sift
Benign
T;T;.;T;.;.
Sift4G
Benign
T;T;T;T;T;T
Polyphen
B;.;B;.;.;.
Vest4
MutPred
Loss of stability (P = 0.0171);.;Loss of stability (P = 0.0171);.;.;.;
MVP
MPC
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