10-24851442-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_020200.7(PRTFDC1):c.576C>A(p.Asn192Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000066 in 151,504 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N192D) has been classified as Likely benign.
Frequency
Consequence
NM_020200.7 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRTFDC1 | NM_020200.7 | c.576C>A | p.Asn192Lys | missense_variant | 8/9 | ENST00000320152.11 | |
PRTFDC1 | NM_001282786.2 | c.554-1551C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRTFDC1 | ENST00000320152.11 | c.576C>A | p.Asn192Lys | missense_variant | 8/9 | 1 | NM_020200.7 | P1 | |
PRTFDC1 | ENST00000376378.5 | c.554-1551C>A | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000660 AC: 1AN: 151504Hom.: 0 Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1459464Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 726042
GnomAD4 genome ? AF: 0.00000660 AC: 1AN: 151504Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 73934
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 09, 2022 | The c.576C>A (p.N192K) alteration is located in exon 8 (coding exon 8) of the PRTFDC1 gene. This alteration results from a C to A substitution at nucleotide position 576, causing the asparagine (N) at amino acid position 192 to be replaced by a lysine (K). 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