14-59745747-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_021136.3(RTN1):c.976G>T(p.Asp326Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.0000775 in 1,613,258 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 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RTN1 | NM_021136.3 | c.976G>T | p.Asp326Tyr | missense_variant | Exon 2 of 9 | ENST00000267484.10 | NP_066959.1 | |
RTN1 | XM_011537063.4 | c.976G>T | p.Asp326Tyr | missense_variant | Exon 2 of 4 | XP_011535365.1 | ||
RTN1 | XM_047431674.1 | c.976G>T | p.Asp326Tyr | missense_variant | Exon 2 of 4 | XP_047287630.1 | ||
RTN1 | XR_007064042.1 | n.1122G>T | non_coding_transcript_exon_variant | Exon 2 of 5 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000342 AC: 52AN: 151994Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000104 AC: 26AN: 249360Hom.: 0 AF XY: 0.0000890 AC XY: 12AN XY: 134806
GnomAD4 exome AF: 0.0000486 AC: 71AN: 1461146Hom.: 0 Cov.: 32 AF XY: 0.0000468 AC XY: 34AN XY: 726878
GnomAD4 genome AF: 0.000355 AC: 54AN: 152112Hom.: 0 Cov.: 32 AF XY: 0.000417 AC XY: 31AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.976G>T (p.D326Y) alteration is located in exon 2 (coding exon 2) of the RTN1 gene. This alteration results from a G to T substitution at nucleotide position 976, causing the aspartic acid (D) at amino acid position 326 to be replaced by a tyrosine (Y). 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