chr19-44878275-G-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6BP7

The ENST00000252485.8(NECTIN2):​c.1095G>T​(p.Val365=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00045 in 1,151,132 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.00033 ( 0 hom., cov: 30)
Exomes 𝑓: 0.00047 ( 0 hom. )

Consequence

NECTIN2
ENST00000252485.8 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.852
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.27).
BP6
Variant 19-44878275-G-T is Benign according to our data. Variant chr19-44878275-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 3045274.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=0.852 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NECTIN2NM_001042724.2 linkuse as main transcriptc.1042+3797G>T intron_variant ENST00000252483.10
NECTIN2NM_002856.3 linkuse as main transcriptc.1095G>T p.Val365= synonymous_variant 6/6
NECTIN2XM_047439169.1 linkuse as main transcriptc.1043-278G>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NECTIN2ENST00000252485.8 linkuse as main transcriptc.1095G>T p.Val365= synonymous_variant 6/61 A2Q92692-2
NECTIN2ENST00000252483.10 linkuse as main transcriptc.1042+3797G>T intron_variant 1 NM_001042724.2 P3Q92692-1
NECTIN2ENST00000585601.1 linkuse as main transcriptc.85-98G>T intron_variant 3
NECTIN2ENST00000591581.1 linkuse as main transcriptc.565-278G>T intron_variant 2

Frequencies

GnomAD3 genomes
AF:
0.000329
AC:
50
AN:
152020
Hom.:
0
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.0000725
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.000288
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000647
Gnomad OTH
AF:
0.000957
GnomAD3 exomes
AF:
0.000231
AC:
29
AN:
125408
Hom.:
0
AF XY:
0.000215
AC XY:
14
AN XY:
65250
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000454
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.0000760
Gnomad NFE exome
AF:
0.000588
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.000468
AC:
468
AN:
999112
Hom.:
0
Cov.:
13
AF XY:
0.000486
AC XY:
245
AN XY:
504340
show subpopulations
Gnomad4 AFR exome
AF:
0.000127
Gnomad4 AMR exome
AF:
0.0000307
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.0000639
Gnomad4 NFE exome
AF:
0.000613
Gnomad4 OTH exome
AF:
0.000360
GnomAD4 genome
AF:
0.000329
AC:
50
AN:
152020
Hom.:
0
Cov.:
30
AF XY:
0.000242
AC XY:
18
AN XY:
74254
show subpopulations
Gnomad4 AFR
AF:
0.0000725
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.000288
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000647
Gnomad4 OTH
AF:
0.000957
Alfa
AF:
0.000412
Hom.:
0
Bravo
AF:
0.000268

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 SciencesNov 01, 2019This 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
BayesDel_noAF
Benign
-0.27
CADD
Benign
20
DANN
Benign
0.72
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

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: rs773661475; hg19: chr19-45381532; API