chr19-44865548-C-T
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001042724.2(NECTIN2):c.366C>T(p.Asp122=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0031 in 1,569,090 control chromosomes in the GnomAD database, including 124 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.016 ( 60 hom., cov: 31)
Exomes 𝑓: 0.0017 ( 64 hom. )
Consequence
NECTIN2
NM_001042724.2 synonymous
NM_001042724.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -6.15
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 Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BP6
Variant 19-44865548-C-T is Benign according to our data. Variant chr19-44865548-C-T is described in ClinVar as [Benign]. Clinvar id is 781489.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-6.15 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.054 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NECTIN2 | NM_001042724.2 | c.366C>T | p.Asp122= | synonymous_variant | 2/9 | ENST00000252483.10 | |
NECTIN2 | NM_002856.3 | c.366C>T | p.Asp122= | synonymous_variant | 2/6 | ||
NECTIN2 | XM_047439169.1 | c.366C>T | p.Asp122= | synonymous_variant | 2/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NECTIN2 | ENST00000252483.10 | c.366C>T | p.Asp122= | synonymous_variant | 2/9 | 1 | NM_001042724.2 | P3 | |
NECTIN2 | ENST00000252485.8 | c.366C>T | p.Asp122= | synonymous_variant | 2/6 | 1 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0159 AC: 2425AN: 152168Hom.: 60 Cov.: 31
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GnomAD3 exomes AF: 0.00402 AC: 714AN: 177630Hom.: 21 AF XY: 0.00301 AC XY: 287AN XY: 95334
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GnomAD4 exome AF: 0.00172 AC: 2435AN: 1416804Hom.: 64 Cov.: 32 AF XY: 0.00146 AC XY: 1021AN XY: 701398
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GnomAD4 genome AF: 0.0159 AC: 2428AN: 152286Hom.: 60 Cov.: 31 AF XY: 0.0156 AC XY: 1162AN XY: 74478
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 31, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at