chr11-119639934-A-C
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000341398.6(NECTIN1):n.1082T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.92 in 1,614,052 control chromosomes in the GnomAD database, including 685,633 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.87 ( 58463 hom., cov: 33)
Exomes 𝑓: 0.93 ( 627170 hom. )
Consequence
NECTIN1
ENST00000341398.6 non_coding_transcript_exon
ENST00000341398.6 non_coding_transcript_exon
Scores
14
Clinical Significance
Conservation
PhyloP100: 0.354
Genes affected
NECTIN1 (HGNC:9706): (nectin cell adhesion molecule 1) This gene encodes an adhesion protein that plays a role in the organization of adherens junctions and tight junctions in epithelial and endothelial cells. The protein is a calcium(2+)-independent cell-cell adhesion molecule that belongs to the immunoglobulin superfamily and has 3 extracellular immunoglobulin-like loops, a single transmembrane domain (in some isoforms), and a cytoplasmic region. This protein acts as a receptor for glycoprotein D (gD) of herpes simplex viruses 1 and 2 (HSV-1, HSV-2), and pseudorabies virus (PRV) and mediates viral entry into epithelial and neuronal cells. Mutations in this gene cause cleft lip and palate/ectodermal dysplasia 1 syndrome (CLPED1) as well as non-syndromic cleft lip with or without cleft palate (CL/P). Alternative splicing results in multiple transcript variants encoding proteins with distinct C-termini. [provided by RefSeq, Oct 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=3.3091562E-6).
BP6
Variant 11-119639934-A-C is Benign according to our data. Variant chr11-119639934-A-C is described in ClinVar as [Benign]. Clinvar id is 802808.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-119639934-A-C is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.959 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NECTIN1 | NM_203285.2 | c.1082T>G | p.Val361Gly | missense_variant | 6/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NECTIN1 | ENST00000341398.6 | n.1082T>G | non_coding_transcript_exon_variant | 6/8 | 1 | ||||
NECTIN1 | ENST00000531468.2 | c.1082T>G | p.Val361Gly | missense_variant | 6/10 | 3 | |||
USP2-AS1 | ENST00000706364.1 | n.953A>C | non_coding_transcript_exon_variant | 5/7 |
Frequencies
GnomAD3 genomes AF: 0.871 AC: 132526AN: 152106Hom.: 58431 Cov.: 33
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GnomAD3 exomes AF: 0.922 AC: 231548AN: 251242Hom.: 107185 AF XY: 0.927 AC XY: 125886AN XY: 135840
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GnomAD4 exome AF: 0.926 AC: 1352931AN: 1461828Hom.: 627170 Cov.: 64 AF XY: 0.928 AC XY: 674746AN XY: 727206
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GnomAD4 genome AF: 0.871 AC: 132612AN: 152224Hom.: 58463 Cov.: 33 AF XY: 0.874 AC XY: 65049AN XY: 74432
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Cleft lip/palate-ectodermal dysplasia syndrome Benign:2
Benign, criteria provided, single submitter | clinical testing | Mendelics | May 28, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Nov 07, 2021 | - - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationTaster
Benign
P
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
ClinPred
T
GERP RS
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at