rs202112717
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_006393.3(NEBL):āc.1302C>Gā(p.Ile434Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000133 in 1,611,798 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I434L) has been classified as Uncertain significance.
Frequency
Consequence
NM_006393.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEBL | NM_006393.3 | c.1302C>G | p.Ile434Met | missense_variant | 13/28 | ENST00000377122.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEBL | ENST00000377122.9 | c.1302C>G | p.Ile434Met | missense_variant | 13/28 | 1 | NM_006393.3 |
Frequencies
GnomAD3 genomes ? AF: 0.000210 AC: 32AN: 152036Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000440 AC: 110AN: 250184Hom.: 1 AF XY: 0.000444 AC XY: 60AN XY: 135262
GnomAD4 exome AF: 0.000125 AC: 183AN: 1459644Hom.: 0 Cov.: 30 AF XY: 0.000114 AC XY: 83AN XY: 726282
GnomAD4 genome ? AF: 0.000210 AC: 32AN: 152154Hom.: 0 Cov.: 32 AF XY: 0.000255 AC XY: 19AN XY: 74420
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 11, 2015 | p.Ile434Met in exon 13 of NEBL: This variant is not expected to have clinical si gnificance because it has been identified in 0.4% (37/8522) of East Asian chromo somes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs202112717). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 15, 2020 | - - |
Primary dilated cardiomyopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 05, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at