3-111072150-C-T
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_015480.3(NECTIN3):c.133C>T(p.Pro45Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000515 in 1,552,238 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Genomes: 𝑓 0.00052 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00051 ( 7 hom. )
Consequence
NECTIN3
NM_015480.3 missense
NM_015480.3 missense
Scores
1
2
15
Clinical Significance
Conservation
PhyloP100: 1.20
Genes affected
NECTIN3 (HGNC:17664): (nectin cell adhesion molecule 3) This gene encodes a member of the nectin family of proteins, which function as adhesion molecules at adherens junctions. This family member interacts with other nectin-like proteins and with afadin, a filamentous actin-binding protein involved in the regulation of directional motility, cell proliferation and survival. This gene plays a role in ocular development involving the ciliary body. Mutations in this gene are believed to result in congenital ocular defects. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.007235378).
BP6
Variant 3-111072150-C-T is Benign according to our data. Variant chr3-111072150-C-T is described in ClinVar as [Benign]. Clinvar id is 3045238.Status of the report is no_assertion_criteria_provided, 0 stars.
BS2
High Homozygotes in GnomAdExome4 at 7 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NECTIN3 | NM_015480.3 | c.133C>T | p.Pro45Ser | missense_variant | 1/6 | ENST00000485303.6 | NP_056295.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NECTIN3 | ENST00000485303.6 | c.133C>T | p.Pro45Ser | missense_variant | 1/6 | 1 | NM_015480.3 | ENSP00000418070.1 |
Frequencies
GnomAD3 genomes AF: 0.000519 AC: 79AN: 152144Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00127 AC: 195AN: 153590Hom.: 3 AF XY: 0.00121 AC XY: 99AN XY: 82086
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GnomAD4 exome AF: 0.000514 AC: 720AN: 1400094Hom.: 7 Cov.: 33 AF XY: 0.000531 AC XY: 367AN XY: 691030
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GnomAD4 genome AF: 0.000519 AC: 79AN: 152144Hom.: 0 Cov.: 32 AF XY: 0.000430 AC XY: 32AN XY: 74338
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
NECTIN3-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 11, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T
M_CAP
Uncertain
D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
PrimateAI
Pathogenic
D
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;D
Sift4G
Benign
T;D
Polyphen
B;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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