14-59607304-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_021136.3(RTN1):c.1954G>A(p.Asp652Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000558 in 1,613,962 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_021136.3 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RTN1 | NM_021136.3 | c.1954G>A | p.Asp652Asn | missense_variant | Exon 4 of 9 | ENST00000267484.10 | NP_066959.1 | |
RTN1 | NM_206852.3 | c.250G>A | p.Asp84Asn | missense_variant | Exon 2 of 7 | NP_996734.1 | ||
RTN1 | NM_001363702.1 | c.205G>A | p.Asp69Asn | missense_variant | Exon 2 of 7 | NP_001350631.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152106Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251062Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135716
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461738Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 4AN XY: 727152
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152224Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74432
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1954G>A (p.D652N) alteration is located in exon 4 (coding exon 4) of the RTN1 gene. This alteration results from a G to A substitution at nucleotide position 1954, causing the aspartic acid (D) at amino acid position 652 to be replaced by an asparagine (N). 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