3-63278698-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001130003.2(SYNPR):c.40C>T(p.Arg14Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000438 in 1,551,528 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001130003.2 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 |
---|---|---|---|---|---|---|---|---|
SYNPR | NM_001130003.2 | c.40C>T | p.Arg14Trp | missense_variant | Exon 2 of 6 | ENST00000478300.6 | NP_001123475.1 | |
SYNPR | XM_017005732.3 | c.40C>T | p.Arg14Trp | missense_variant | Exon 2 of 6 | XP_016861221.1 | ||
SYNPR | XM_017005731.1 | c.132+26112C>T | intron_variant | Intron 2 of 5 | XP_016861220.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152126Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000260 AC: 4AN: 154022Hom.: 0 AF XY: 0.0000122 AC XY: 1AN XY: 81740
GnomAD4 exome AF: 0.0000436 AC: 61AN: 1399402Hom.: 0 Cov.: 31 AF XY: 0.0000362 AC XY: 25AN XY: 690212
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152126Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74308
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.40C>T (p.R14W) alteration is located in exon 2 (coding exon 2) of the SYNPR gene. This alteration results from a C to T substitution at nucleotide position 40, causing the arginine (R) at amino acid position 14 to be replaced by a tryptophan (W). 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