chr2-151485804-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP6
The NM_001164507.2(NEB):c.25534G>A(p.Gly8512Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000992 in 1,613,382 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G8512R) has been classified as Likely benign.
Frequency
Consequence
NM_001164507.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEB | NM_001164507.2 | c.25534G>A | p.Gly8512Ser | missense_variant | 182/182 | ENST00000427231.7 | |
NEB | NM_001164508.2 | c.25534G>A | p.Gly8512Ser | missense_variant | 182/182 | ENST00000397345.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.25534G>A | p.Gly8512Ser | missense_variant | 182/182 | 5 | NM_001164508.2 | P5 | |
NEB | ENST00000427231.7 | c.25534G>A | p.Gly8512Ser | missense_variant | 182/182 | 5 | NM_001164507.2 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000563 AC: 14AN: 248620Hom.: 0 AF XY: 0.0000371 AC XY: 5AN XY: 134798
GnomAD4 exome AF: 0.00000890 AC: 13AN: 1461198Hom.: 0 Cov.: 31 AF XY: 0.00000826 AC XY: 6AN XY: 726814
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152184Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74344
ClinVar
Submissions by phenotype
Nemaline myopathy 2 Uncertain:1Benign:1
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Dec 14, 2020 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 28, 2023 | - - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 15, 2023 | The c.19966G>A (p.G6656S) alteration is located in exon 150 (coding exon 148) of the NEB gene. This alteration results from a G to A substitution at nucleotide position 19966, causing the glycine (G) at amino acid position 6656 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at