chr1-77916097-T-C
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_144573.4(NEXN):c.-10T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000436 in 1,604,986 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 (★).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000028 ( 0 hom. )
Consequence
NEXN
NM_144573.4 5_prime_UTR
NM_144573.4 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.79
Genes affected
NEXN (HGNC:29557): (nexilin F-actin binding protein) This gene encodes a filamentous actin-binding protein that may function in cell adhesion and migration. Mutations in this gene have been associated with dilated cardiomyopathy, also known as CMD1CC. Alternatively spliced transcript variants have been described.[provided by RefSeq, Feb 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NEXN | NM_144573.4 | c.-10T>C | 5_prime_UTR_variant | 2/13 | ENST00000334785.12 | NP_653174.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NEXN | ENST00000334785.12 | c.-10T>C | 5_prime_UTR_variant | 2/13 | 1 | NM_144573.4 | ENSP00000333938 | P3 | ||
NEXN | ENST00000401035.7 | c.-10T>C | 5_prime_UTR_variant | 2/9 | 1 | ENSP00000383814 | ||||
NEXN | ENST00000330010.12 | c.-10T>C | 5_prime_UTR_variant | 2/12 | 2 | ENSP00000327363 | A1 | |||
NEXN | ENST00000440324.5 | c.-10T>C | 5_prime_UTR_variant | 2/10 | 5 | ENSP00000411902 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 151914Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00000404 AC: 1AN: 247630Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134364
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GnomAD4 exome AF: 0.00000275 AC: 4AN: 1453072Hom.: 0 Cov.: 28 AF XY: 0.00000138 AC XY: 1AN XY: 723020
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GnomAD4 genome AF: 0.0000197 AC: 3AN: 151914Hom.: 0 Cov.: 33 AF XY: 0.0000270 AC XY: 2AN XY: 74198
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jul 24, 2014 | - - |
Computational scores
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BayesDel_noAF
Benign
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Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at