rs768693028
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 2P and 20B. PM2BP4_StrongBP6_Very_StrongBS1BS2
The NM_001164507.2(NEB):c.21862G>C(p.Glu7288Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000825 in 1,599,100 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 Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E7288G) has been classified as Likely benign.
Frequency
Consequence
NM_001164507.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEB | NM_001164507.2 | c.21862G>C | p.Glu7288Gln | missense_variant | 148/182 | ENST00000427231.7 | |
NEB | NM_001164508.2 | c.21862G>C | p.Glu7288Gln | missense_variant | 148/182 | ENST00000397345.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.21862G>C | p.Glu7288Gln | missense_variant | 148/182 | 5 | NM_001164508.2 | P5 | |
NEB | ENST00000427231.7 | c.21862G>C | p.Glu7288Gln | missense_variant | 148/182 | 5 | NM_001164507.2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000495 AC: 112AN: 226240Hom.: 2 AF XY: 0.000362 AC XY: 44AN XY: 121662
GnomAD4 exome AF: 0.0000892 AC: 129AN: 1446942Hom.: 0 Cov.: 30 AF XY: 0.0000738 AC XY: 53AN XY: 718056
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152158Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74316
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 05, 2021 | - - |
Nemaline myopathy 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at