10-94352963-T-A

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate

The NM_022451.11(NOC3L):​c.791A>T​(p.Glu264Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Consequence

NOC3L
NM_022451.11 missense

Scores

7
8
4

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 7.67
Variant links:
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 4 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.842

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NOC3LNM_022451.11 linkuse as main transcriptc.791A>T p.Glu264Val missense_variant 7/21 ENST00000371361.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NOC3LENST00000371361.3 linkuse as main transcriptc.791A>T p.Glu264Val missense_variant 7/211 NM_022451.11 P1
NOC3LENST00000463649.5 linkuse as main transcriptn.1643A>T non_coding_transcript_exon_variant 6/102

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
32

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 GeneticsDec 27, 2023The c.791A>T (p.E264V) alteration is located in exon 7 (coding exon 7) of the NOC3L gene. This alteration results from a A to T substitution at nucleotide position 791, causing the glutamic acid (E) at amino acid position 264 to be replaced by a valine (V). 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
Uncertain
0.50
BayesDel_addAF
Pathogenic
0.24
D
BayesDel_noAF
Uncertain
0.11
CADD
Pathogenic
33
DANN
Uncertain
0.99
DEOGEN2
Benign
0.058
T
Eigen
Pathogenic
0.74
Eigen_PC
Pathogenic
0.70
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Uncertain
0.93
D
M_CAP
Benign
0.058
D
MetaRNN
Pathogenic
0.84
D
MetaSVM
Benign
-0.68
T
MutationAssessor
Uncertain
2.6
M
MutationTaster
Benign
1.0
D;D;D
PrimateAI
Uncertain
0.67
T
PROVEAN
Pathogenic
-5.7
D
REVEL
Uncertain
0.43
Sift
Pathogenic
0.0
D
Sift4G
Uncertain
0.024
D
Polyphen
1.0
D
Vest4
0.94
MutPred
0.62
Gain of MoRF binding (P = 0.0325);
MVP
0.54
MPC
0.46
ClinPred
1.0
D
GERP RS
5.1
Varity_R
0.82
gMVP
0.58

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.21
Details are displayed if max score is > 0.2
DS_DG_spliceai
0.21
Position offset: 20

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs758954884; hg19: chr10-96112720; API