2-151490409-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6BP7
The NM_001164507.2(NEB):c.25260G>A(p.Ser8420=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000157 in 1,596,390 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 Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. S8420S) has been classified as Likely benign.
Frequency
Consequence
NM_001164507.2 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEB | NM_001164507.2 | c.25260G>A | p.Ser8420= | synonymous_variant | 180/182 | ENST00000427231.7 | |
NEB | NM_001164508.2 | c.25260G>A | p.Ser8420= | synonymous_variant | 180/182 | ENST00000397345.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.25260G>A | p.Ser8420= | synonymous_variant | 180/182 | 5 | NM_001164508.2 | P5 | |
NEB | ENST00000427231.7 | c.25260G>A | p.Ser8420= | synonymous_variant | 180/182 | 5 | NM_001164507.2 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152162Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000135 AC: 3AN: 221762Hom.: 0 AF XY: 0.00000837 AC XY: 1AN XY: 119442
GnomAD4 exome AF: 0.0000111 AC: 16AN: 1444228Hom.: 0 Cov.: 30 AF XY: 0.00000698 AC XY: 5AN XY: 716508
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152162Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74324
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Oct 06, 2020 | - - |
NEB-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 13, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Nemaline myopathy 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at