17-48721857-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_032391.3(PRAC1):c.118G>A(p.Asp40Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00114 in 1,541,592 control chromosomes in the GnomAD database, including 25 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_032391.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRAC1 | NM_032391.3 | c.118G>A | p.Asp40Asn | missense_variant | Exon 2 of 2 | ENST00000290294.5 | NP_115767.1 | |
PRAC2 | XM_011524747.2 | c.-84+984C>T | intron_variant | Intron 1 of 1 | XP_011523049.1 | |||
PRAC2 | XM_047435918.1 | c.-83-2471C>T | intron_variant | Intron 1 of 1 | XP_047291874.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00582 AC: 886AN: 152236Hom.: 12 Cov.: 32
GnomAD3 exomes AF: 0.00137 AC: 207AN: 150952Hom.: 1 AF XY: 0.000817 AC XY: 65AN XY: 79534
GnomAD4 exome AF: 0.000626 AC: 870AN: 1389238Hom.: 13 Cov.: 30 AF XY: 0.000553 AC XY: 379AN XY: 684856
GnomAD4 genome AF: 0.00581 AC: 885AN: 152354Hom.: 12 Cov.: 32 AF XY: 0.00562 AC XY: 419AN XY: 74502
ClinVar
Submissions by phenotype
not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at