chr19-44865309-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001042724.2(NECTIN2):c.127C>T(p.Arg43Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,342 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001042724.2 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NECTIN2 | NM_001042724.2 | c.127C>T | p.Arg43Ter | stop_gained | 2/9 | ENST00000252483.10 | |
NECTIN2 | NM_002856.3 | c.127C>T | p.Arg43Ter | stop_gained | 2/6 | ||
NECTIN2 | XM_047439169.1 | c.127C>T | p.Arg43Ter | stop_gained | 2/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NECTIN2 | ENST00000252483.10 | c.127C>T | p.Arg43Ter | stop_gained | 2/9 | 1 | NM_001042724.2 | P3 | |
NECTIN2 | ENST00000252485.8 | c.127C>T | p.Arg43Ter | stop_gained | 2/6 | 1 | A2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461342Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 726950
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Cerebral palsy Uncertain:1
Uncertain significance, criteria provided, single submitter | research | Neurogenetics Research Program, University of Adelaide | Jun 10, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.