chr11-47442706-C-A
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_005055.5(RAPSN):c.640G>T(p.Val214Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,886 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V214M) has been classified as Likely benign.
Frequency
Consequence
NM_005055.5 missense
Scores
Clinical Significance
Conservation
Publications
- fetal akinesia deformation sequence 2Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
- neuromuscular diseaseInheritance: AR Classification: DEFINITIVE Submitted by: Ambry Genetics
- congenital myasthenic syndrome 11Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), PanelApp Australia, Genomics England PanelApp
- fetal akinesia deformation sequence 1Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- postsynaptic congenital myasthenic syndromeInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RAPSN | NM_005055.5 | c.640G>T | p.Val214Leu | missense_variant | Exon 3 of 8 | ENST00000298854.7 | NP_005046.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RAPSN | ENST00000298854.7 | c.640G>T | p.Val214Leu | missense_variant | Exon 3 of 8 | 1 | NM_005055.5 | ENSP00000298854.2 | ||
RAPSN | ENST00000352508.7 | c.640G>T | p.Val214Leu | missense_variant | Exon 3 of 6 | 1 | ENSP00000298853.3 | |||
RAPSN | ENST00000529341.1 | c.640G>T | p.Val214Leu | missense_variant | Exon 3 of 5 | 1 | ENSP00000431732.1 | |||
RAPSN | ENST00000524487.5 | c.532-785G>T | intron_variant | Intron 2 of 6 | 5 | ENSP00000435551.2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461886Hom.: 0 Cov.: 34 AF XY: 0.00000138 AC XY: 1AN XY: 727242 show subpopulations
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at