rs762220487
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 4P and 2B. PM2PP3_ModerateBP6_Moderate
The NM_001164507.2(NEB):c.23425C>T(p.Arg7809Trp) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000267 in 1,609,764 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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. R7809Q) 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 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEB | NM_001164507.2 | c.23425C>T | p.Arg7809Trp | missense_variant | 162/182 | ENST00000427231.7 | |
NEB | NM_001164508.2 | c.23425C>T | p.Arg7809Trp | missense_variant | 162/182 | ENST00000397345.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.23425C>T | p.Arg7809Trp | missense_variant | 162/182 | 5 | NM_001164508.2 | P5 | |
NEB | ENST00000427231.7 | c.23425C>T | p.Arg7809Trp | missense_variant | 162/182 | 5 | NM_001164507.2 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152110Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000165 AC: 4AN: 243154Hom.: 0 AF XY: 0.0000228 AC XY: 3AN XY: 131800
GnomAD4 exome AF: 0.0000268 AC: 39AN: 1457654Hom.: 0 Cov.: 30 AF XY: 0.0000166 AC XY: 12AN XY: 724728
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152110Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74288
ClinVar
Submissions by phenotype
Nemaline myopathy 2 Uncertain:1Benign:1
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Jan 17, 2020 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 10, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at