10-24856937-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_020200.7(PRTFDC1):c.482A>G(p.Lys161Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000341 in 1,613,564 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020200.7 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRTFDC1 | NM_020200.7 | c.482A>G | p.Lys161Arg | missense_variant | 6/9 | ENST00000320152.11 | |
PRTFDC1 | NM_001282786.2 | c.482A>G | p.Lys161Arg | missense_variant | 6/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRTFDC1 | ENST00000320152.11 | c.482A>G | p.Lys161Arg | missense_variant | 6/9 | 1 | NM_020200.7 | P1 | |
PRTFDC1 | ENST00000376378.5 | c.482A>G | p.Lys161Arg | missense_variant | 6/8 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000145 AC: 22AN: 152198Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251356Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135840
GnomAD4 exome AF: 0.0000219 AC: 32AN: 1461248Hom.: 0 Cov.: 30 AF XY: 0.0000206 AC XY: 15AN XY: 726990
GnomAD4 genome ? AF: 0.000151 AC: 23AN: 152316Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74490
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 09, 2021 | The c.482A>G (p.K161R) alteration is located in exon 6 (coding exon 6) of the PRTFDC1 gene. This alteration results from a A to G substitution at nucleotide position 482, causing the lysine (K) at amino acid position 161 to be replaced by an arginine (R). 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