1-77916106-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_144573.4(NEXN):c.-1C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_144573.4 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NEXN | ENST00000334785 | c.-1C>T | 5_prime_UTR_variant | Exon 2 of 13 | 1 | NM_144573.4 | ENSP00000333938.7 | |||
NEXN | ENST00000401035 | c.-1C>T | 5_prime_UTR_variant | Exon 2 of 9 | 1 | ENSP00000383814.3 | ||||
NEXN | ENST00000330010 | c.-1C>T | 5_prime_UTR_variant | Exon 2 of 12 | 2 | ENSP00000327363.8 | ||||
NEXN | ENST00000440324 | c.-1C>T | 5_prime_UTR_variant | Exon 2 of 10 | 5 | ENSP00000411902.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 1454920Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0AN XY: 723878
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Cardiovascular phenotype Uncertain:1
The c.-1C>T variant is located in the 5' untranslated region (5’ UTR) of the NEXN gene. This variant results from a C to T substitution 1 bases upstream from the first translated codon. This nucleotide position is well conserved in available vertebrate species. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at