chr10-24851444-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_020200.7(PRTFDC1):c.574A>G(p.Asn192Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000822 in 1,459,696 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N192K) has been classified as Uncertain significance.
Frequency
Consequence
NM_020200.7 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRTFDC1 | NM_020200.7 | c.574A>G | p.Asn192Asp | missense_variant | 8/9 | ENST00000320152.11 | |
PRTFDC1 | NM_001282786.2 | c.554-1553A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRTFDC1 | ENST00000320152.11 | c.574A>G | p.Asn192Asp | missense_variant | 8/9 | 1 | NM_020200.7 | P1 | |
PRTFDC1 | ENST00000376378.5 | c.554-1553A>G | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000683 AC: 17AN: 248882Hom.: 0 AF XY: 0.0000371 AC XY: 5AN XY: 134602
GnomAD4 exome AF: 0.00000822 AC: 12AN: 1459696Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 726158
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 18, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at