chr10-24937333-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_020200.7(PRTFDC1):āc.190A>Gā(p.Ile64Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,612,150 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 (ā ).
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.190A>G | p.Ile64Val | missense_variant | 3/9 | ENST00000320152.11 | |
PRTFDC1 | NM_001282786.2 | c.190A>G | p.Ile64Val | missense_variant | 3/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRTFDC1 | ENST00000320152.11 | c.190A>G | p.Ile64Val | missense_variant | 3/9 | 1 | NM_020200.7 | P1 | |
PRTFDC1 | ENST00000376378.5 | c.190A>G | p.Ile64Val | missense_variant | 3/8 | 2 | |||
PRTFDC1 | ENST00000376376.3 | c.190A>G | p.Ile64Val | missense_variant | 3/4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152186Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000402 AC: 10AN: 248628Hom.: 0 AF XY: 0.0000372 AC XY: 5AN XY: 134252
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1459964Hom.: 0 Cov.: 31 AF XY: 0.00000964 AC XY: 7AN XY: 726068
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152186Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 21, 2023 | The c.190A>G (p.I64V) alteration is located in exon 3 (coding exon 3) of the PRTFDC1 gene. This alteration results from a A to G substitution at nucleotide position 190, causing the isoleucine (I) at amino acid position 64 to be replaced by a valine (V). 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