chr1-77916073-C-A
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_144573.4(NEXN):c.-34C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000518 in 1,543,390 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 Benign (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000050 ( 0 hom. )
Consequence
NEXN
NM_144573.4 5_prime_UTR
NM_144573.4 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.572
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 Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.69).
BP6
Variant 1-77916073-C-A is Benign according to our data. Variant chr1-77916073-C-A is described in ClinVar as [Benign]. Clinvar id is 201912.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAdExome4 at 7 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEXN | NM_144573.4 | c.-34C>A | 5_prime_UTR_variant | 2/13 | ENST00000334785.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEXN | ENST00000334785.12 | c.-34C>A | 5_prime_UTR_variant | 2/13 | 1 | NM_144573.4 | P3 | ||
NEXN | ENST00000401035.7 | c.-34C>A | 5_prime_UTR_variant | 2/9 | 1 | ||||
NEXN | ENST00000330010.12 | c.-34C>A | 5_prime_UTR_variant | 2/12 | 2 | A1 | |||
NEXN | ENST00000440324.5 | c.-34C>A | 5_prime_UTR_variant | 2/10 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000660 AC: 1AN: 151630Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.00000503 AC: 7AN: 1391760Hom.: 0 Cov.: 26 AF XY: 0.00000434 AC XY: 3AN XY: 691332
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GnomAD4 genome AF: 0.00000660 AC: 1AN: 151630Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74020
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 23, 2014 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at