1-77916073-C-A
Position:
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]
Genome browser will be placed here
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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NEXN | NM_144573.4 | c.-34C>A | 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.-34C>A | 5_prime_UTR_variant | 2/13 | 1 | NM_144573.4 | ENSP00000333938 | P3 | ||
NEXN | ENST00000401035.7 | c.-34C>A | 5_prime_UTR_variant | 2/9 | 1 | ENSP00000383814 | ||||
NEXN | ENST00000330010.12 | c.-34C>A | 5_prime_UTR_variant | 2/12 | 2 | ENSP00000327363 | A1 | |||
NEXN | ENST00000440324.5 | c.-34C>A | 5_prime_UTR_variant | 2/10 | 5 | ENSP00000411902 |
Frequencies
GnomAD3 genomes AF: 0.00000660 AC: 1AN: 151630Hom.: 0 Cov.: 32
GnomAD3 genomes
AF:
AC:
1
AN:
151630
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.00000503 AC: 7AN: 1391760Hom.: 0 Cov.: 26 AF XY: 0.00000434 AC XY: 3AN XY: 691332
GnomAD4 exome
AF:
AC:
7
AN:
1391760
Hom.:
Cov.:
26
AF XY:
AC XY:
3
AN XY:
691332
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.00000660 AC: 1AN: 151630Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74020
GnomAD4 genome
AF:
AC:
1
AN:
151630
Hom.:
Cov.:
32
AF XY:
AC XY:
0
AN XY:
74020
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Bravo
AF:
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
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at