10-94334716-G-A
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_022451.11(NOC3L):c.2192C>T(p.Ser731Phe) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000249 in 1,607,640 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000026 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000025 ( 0 hom. )
Consequence
NOC3L
NM_022451.11 missense, splice_region
NM_022451.11 missense, splice_region
Scores
1
10
8
Clinical Significance
Conservation
PhyloP100: 8.72
Genes affected
NOC3L (HGNC:24034): (NOC3 like DNA replication regulator) Enables RNA binding activity. Predicted to be involved in DNA replication initiation. Predicted to act upstream of or within fat cell differentiation. Located in mitochondrion; nucleolus; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NOC3L | NM_022451.11 | c.2192C>T | p.Ser731Phe | missense_variant, splice_region_variant | 20/21 | ENST00000371361.3 | |
NOC3L | XR_002957007.2 | n.2293C>T | splice_region_variant, non_coding_transcript_exon_variant | 20/22 | |||
NOC3L | XR_007061982.1 | n.2293C>T | splice_region_variant, non_coding_transcript_exon_variant | 20/22 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NOC3L | ENST00000371361.3 | c.2192C>T | p.Ser731Phe | missense_variant, splice_region_variant | 20/21 | 1 | NM_022451.11 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152096Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000242 AC: 6AN: 248196Hom.: 0 AF XY: 0.0000298 AC XY: 4AN XY: 134090
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GnomAD4 exome AF: 0.0000247 AC: 36AN: 1455544Hom.: 0 Cov.: 29 AF XY: 0.0000221 AC XY: 16AN XY: 724220
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GnomAD4 genome AF: 0.0000263 AC: 4AN: 152096Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 4AN XY: 74276
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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 | Jan 27, 2022 | The c.2192C>T (p.S731F) alteration is located in exon 20 (coding exon 20) of the NOC3L gene. This alteration results from a C to T substitution at nucleotide position 2192, causing the serine (S) at amino acid position 731 to be replaced by a phenylalanine (F). 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
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D
M_CAP
Benign
T
MetaRNN
Uncertain
T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
MutationTaster
Benign
D;D;D
PrimateAI
Benign
T
PROVEAN
Uncertain
D
REVEL
Uncertain
Sift
Uncertain
D
Sift4G
Uncertain
D
Polyphen
P
Vest4
MutPred
Loss of phosphorylation at S731 (P = 0.0068);
MVP
MPC
ClinPred
D
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