chr19-44872038-C-T

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

Scores

10
8

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.81
Variant links:
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
NECTIN2NM_001042724.2 linkuse as main transcriptc.664C>T p.Arg222Cys missense_variant 3/9 ENST00000252483.10
NECTIN2NM_002856.3 linkuse as main transcriptc.664C>T p.Arg222Cys missense_variant 3/6
NECTIN2XM_047439169.1 linkuse as main transcriptc.664C>T p.Arg222Cys missense_variant 3/6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NECTIN2ENST00000252483.10 linkuse as main transcriptc.664C>T p.Arg222Cys missense_variant 3/91 NM_001042724.2 P3Q92692-1
NECTIN2ENST00000252485.8 linkuse as main transcriptc.664C>T p.Arg222Cys missense_variant 3/61 A2Q92692-2
NECTIN2ENST00000591581.1 linkuse as main transcriptc.187C>T p.Arg63Cys missense_variant 1/42

Frequencies

GnomAD3 genomes
AF:
0.00181
AC:
275
AN:
152154
Hom.:
1
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.00640
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000262
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000294
Gnomad OTH
AF:
0.00144
GnomAD3 exomes
AF:
0.000465
AC:
117
AN:
251466
Hom.:
0
AF XY:
0.000280
AC XY:
38
AN XY:
135914
show subpopulations
Gnomad AFR exome
AF:
0.00572
Gnomad AMR exome
AF:
0.000318
Gnomad ASJ exome
AF:
0.0000992
Gnomad EAS exome
AF:
0.000109
Gnomad SAS exome
AF:
0.000196
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000264
Gnomad OTH exome
AF:
0.000163
GnomAD4 exome
AF:
0.000184
AC:
269
AN:
1461890
Hom.:
0
Cov.:
32
AF XY:
0.000162
AC XY:
118
AN XY:
727246
show subpopulations
Gnomad4 AFR exome
AF:
0.00585
Gnomad4 AMR exome
AF:
0.000380
Gnomad4 ASJ exome
AF:
0.0000383
Gnomad4 EAS exome
AF:
0.0000756
Gnomad4 SAS exome
AF:
0.000128
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000189
Gnomad4 OTH exome
AF:
0.000331
GnomAD4 genome
AF:
0.00181
AC:
275
AN:
152272
Hom.:
1
Cov.:
31
AF XY:
0.00157
AC XY:
117
AN XY:
74454
show subpopulations
Gnomad4 AFR
AF:
0.00638
Gnomad4 AMR
AF:
0.000262
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000294
Gnomad4 OTH
AF:
0.00142
Alfa
AF:
0.000287
Hom.:
0
Bravo
AF:
0.00210
ESP6500AA
AF:
0.00545
AC:
24
ESP6500EA
AF:
0.000116
AC:
1
ExAC
AF:
0.000552
AC:
67

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 submitterclinical testingPreventionGenetics, part of Exact SciencesMay 06, 2022This 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: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.23
BayesDel_addAF
Benign
-0.19
T
BayesDel_noAF
Uncertain
-0.040
CADD
Uncertain
25
DANN
Uncertain
1.0
DEOGEN2
Uncertain
0.67
.;D
Eigen
Uncertain
0.24
Eigen_PC
Uncertain
0.28
FATHMM_MKL
Uncertain
0.89
D
LIST_S2
Benign
0.81
T;T
M_CAP
Benign
0.077
D
MetaRNN
Benign
0.013
T;T
MetaSVM
Uncertain
-0.27
T
MutationTaster
Benign
1.0
D;D
PrimateAI
Benign
0.42
T
PROVEAN
Uncertain
-2.4
N;N
REVEL
Uncertain
0.57
Sift
Benign
0.17
T;T
Sift4G
Uncertain
0.056
T;T
Polyphen
0.39
B;P
Vest4
0.45
MVP
0.75
MPC
0.82
ClinPred
0.036
T
GERP RS
4.3
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.13
gMVP
0.77

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: rs148321526; hg19: chr19-45375295; API