14-59607367-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_021136.3(RTN1):c.1891G>A(p.Ala631Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000118 in 1,613,660 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 Uncertain significance (★).
Frequency
Consequence
NM_021136.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RTN1 | NM_021136.3 | c.1891G>A | p.Ala631Thr | missense_variant | Exon 4 of 9 | ENST00000267484.10 | NP_066959.1 | |
RTN1 | NM_206852.3 | c.187G>A | p.Ala63Thr | missense_variant | Exon 2 of 7 | NP_996734.1 | ||
RTN1 | NM_001363702.1 | c.142G>A | p.Ala48Thr | missense_variant | Exon 2 of 7 | NP_001350631.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151698Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251242Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135788
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461846Hom.: 0 Cov.: 32 AF XY: 0.00000688 AC XY: 5AN XY: 727214
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151814Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74186
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1891G>A (p.A631T) 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 1891, causing the alanine (A) at amino acid position 631 to be replaced by a threonine (T). 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