chr1-77917581-T-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_144573.4(NEXN):āc.43T>Cā(p.Ser15Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000548 in 1,460,798 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 Uncertain significance (ā ).
Frequency
Consequence
NM_144573.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NEXN | NM_144573.4 | c.43T>C | p.Ser15Pro | missense_variant | 3/13 | ENST00000334785.12 | NP_653174.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NEXN | ENST00000334785.12 | c.43T>C | p.Ser15Pro | missense_variant | 3/13 | 1 | NM_144573.4 | ENSP00000333938 | P3 | |
NEXN | ENST00000401035.7 | c.28-379T>C | intron_variant | 1 | ENSP00000383814 | |||||
NEXN | ENST00000440324.5 | c.43T>C | p.Ser15Pro | missense_variant | 3/10 | 5 | ENSP00000411902 | |||
NEXN | ENST00000330010.12 | c.28-379T>C | intron_variant | 2 | ENSP00000327363 | A1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000548 AC: 8AN: 1460798Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 726708
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Cardiomyopathy Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario | Mar 16, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.