2-151663631-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_001164507.2(NEB):c.5680A>T(p.Arg1894Trp) variant causes a missense change. The variant allele was found at a frequency of 0.0000149 in 1,613,846 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. R1894G) has been classified as Uncertain significance.
Frequency
Consequence
NM_001164507.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEB | NM_001164507.2 | c.5680A>T | p.Arg1894Trp | missense_variant | 45/182 | ENST00000427231.7 | |
NEB | NM_001164508.2 | c.5680A>T | p.Arg1894Trp | missense_variant | 45/182 | ENST00000397345.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.5680A>T | p.Arg1894Trp | missense_variant | 45/182 | 5 | NM_001164508.2 | P5 | |
NEB | ENST00000427231.7 | c.5680A>T | p.Arg1894Trp | missense_variant | 45/182 | 5 | NM_001164507.2 | A2 | |
NEB | ENST00000409198.5 | c.5680A>T | p.Arg1894Trp | missense_variant | 45/150 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152212Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000402 AC: 10AN: 249026Hom.: 0 AF XY: 0.0000444 AC XY: 6AN XY: 135102
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461516Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 727044
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152330Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74488
ClinVar
Submissions by phenotype
Nemaline myopathy 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 21, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at