chr15-73052719-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_002499.4(NEO1):​c.44C>T​(p.Ser15Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 30)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

NEO1
NM_002499.4 missense

Scores

2
2
15

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.11
Variant links:
Genes affected
NEO1 (HGNC:7754): (neogenin 1) This gene encodes a cell surface protein that is a member of the immunoglobulin superfamily. The encoded protein consists of four N-terminal immunoglobulin-like domains, six fibronectin type III domains, a transmembrane domain and a C-terminal internal domain that shares homology with the tumor suppressor candidate gene DCC. This protein may be involved in cell growth and differentiation and in cell-cell adhesion. Defects in this gene are associated with cell proliferation in certain cancers. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Feb 2010]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.21267417).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NEO1NM_002499.4 linkc.44C>T p.Ser15Phe missense_variant Exon 1 of 29 ENST00000261908.11 NP_002490.2 Q92859-1Q59FP8

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NEO1ENST00000261908.11 linkc.44C>T p.Ser15Phe missense_variant Exon 1 of 29 1 NM_002499.4 ENSP00000261908.6 Q92859-1
NEO1ENST00000558964.5 linkc.44C>T p.Ser15Phe missense_variant Exon 1 of 28 1 ENSP00000453200.1 Q92859-4
NEO1ENST00000560262.5 linkc.44C>T p.Ser15Phe missense_variant Exon 1 of 28 1 ENSP00000453317.1 Q92859-3
NEO1ENST00000339362.9 linkc.44C>T p.Ser15Phe missense_variant Exon 2 of 30 5 ENSP00000341198.5 Q92859-1

Frequencies

GnomAD3 genomes
Cov.:
30
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1207832
Hom.:
0
Cov.:
30
AF XY:
0.00
AC XY:
0
AN XY:
595256
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.24
BayesDel_addAF
Benign
-0.086
T
BayesDel_noAF
Benign
-0.36
CADD
Benign
18
DANN
Uncertain
0.99
DEOGEN2
Benign
0.091
T;T;.;.
Eigen
Benign
-0.78
Eigen_PC
Benign
-0.80
FATHMM_MKL
Benign
0.035
N
LIST_S2
Benign
0.80
.;T;T;T
M_CAP
Pathogenic
0.68
D
MetaRNN
Benign
0.21
T;T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.0
N;N;N;N
PrimateAI
Pathogenic
0.91
D
PROVEAN
Benign
-0.040
N;N;N;N
REVEL
Benign
0.081
Sift
Benign
0.077
T;T;T;T
Sift4G
Uncertain
0.025
D;D;D;D
Polyphen
0.68
P;P;.;.
Vest4
0.27
MutPred
0.48
Loss of sheet (P = 3e-04);Loss of sheet (P = 3e-04);Loss of sheet (P = 3e-04);Loss of sheet (P = 3e-04);
MVP
0.58
MPC
0.20
ClinPred
0.12
T
GERP RS
0.013
Varity_R
0.069
gMVP
0.43

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs748943546; hg19: chr15-73345060; API