chr19-44872038-C-T
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_001042724.2(NECTIN2):c.664C>T(p.Arg222Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000337 in 1,614,162 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.0018 ( 1 hom., cov: 31)
Exomes 𝑓: 0.00018 ( 0 hom. )
Consequence
NECTIN2
NM_001042724.2 missense
NM_001042724.2 missense
Scores
10
8
Clinical Significance
Conservation
PhyloP100: 2.81
Genes affected
NECTIN2 (HGNC:9707): (nectin cell adhesion molecule 2) This gene encodes a single-pass type I membrane glycoprotein with two Ig-like C2-type domains and an Ig-like V-type domain. This protein is one of the plasma membrane components of adherens junctions. It also serves as an entry for certain mutant strains of herpes simplex virus and pseudorabies virus, and it is involved in cell to cell spreading of these viruses. Variations in this gene have been associated with differences in the severity of multiple sclerosis. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.013333887).
BP6
Variant 19-44872038-C-T is Benign according to our data. Variant chr19-44872038-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3038754.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NECTIN2 | NM_001042724.2 | c.664C>T | p.Arg222Cys | missense_variant | 3/9 | ENST00000252483.10 | |
NECTIN2 | NM_002856.3 | c.664C>T | p.Arg222Cys | missense_variant | 3/6 | ||
NECTIN2 | XM_047439169.1 | c.664C>T | p.Arg222Cys | missense_variant | 3/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NECTIN2 | ENST00000252483.10 | c.664C>T | p.Arg222Cys | missense_variant | 3/9 | 1 | NM_001042724.2 | P3 | |
NECTIN2 | ENST00000252485.8 | c.664C>T | p.Arg222Cys | missense_variant | 3/6 | 1 | A2 | ||
NECTIN2 | ENST00000591581.1 | c.187C>T | p.Arg63Cys | missense_variant | 1/4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00181 AC: 275AN: 152154Hom.: 1 Cov.: 31
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GnomAD3 exomes AF: 0.000465 AC: 117AN: 251466Hom.: 0 AF XY: 0.000280 AC XY: 38AN XY: 135914
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GnomAD4 exome AF: 0.000184 AC: 269AN: 1461890Hom.: 0 Cov.: 32 AF XY: 0.000162 AC XY: 118AN XY: 727246
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GnomAD4 genome AF: 0.00181 AC: 275AN: 152272Hom.: 1 Cov.: 31 AF XY: 0.00157 AC XY: 117AN XY: 74454
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
NECTIN2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 06, 2022 | This variant is classified as likely 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
Uncertain
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Uncertain
.;D
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T
M_CAP
Benign
D
MetaRNN
Benign
T;T
MetaSVM
Uncertain
T
MutationTaster
Benign
D;D
PrimateAI
Benign
T
PROVEAN
Uncertain
N;N
REVEL
Uncertain
Sift
Benign
T;T
Sift4G
Uncertain
T;T
Polyphen
B;P
Vest4
MVP
MPC
0.82
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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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