4-118316204-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_003619.4(PRSS12):c.1270G>A(p.Val424Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000936 in 1,613,994 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. V424V) has been classified as Benign.
Frequency
Consequence
NM_003619.4 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRSS12 | NM_003619.4 | c.1270G>A | p.Val424Ile | missense_variant | 6/13 | ENST00000296498.3 | |
PRSS12 | XM_011532387.3 | c.1270G>A | p.Val424Ile | missense_variant | 6/9 | ||
PRSS12 | XM_005263318.5 | c.1270G>A | p.Val424Ile | missense_variant | 6/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRSS12 | ENST00000296498.3 | c.1270G>A | p.Val424Ile | missense_variant | 6/13 | 1 | NM_003619.4 | P1 | |
PRSS12 | ENST00000503043.1 | n.298G>A | non_coding_transcript_exon_variant | 2/3 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00524 AC: 796AN: 152040Hom.: 14 Cov.: 31
GnomAD3 exomes AF: 0.00133 AC: 335AN: 251284Hom.: 4 AF XY: 0.000957 AC XY: 130AN XY: 135784
GnomAD4 exome AF: 0.000488 AC: 713AN: 1461836Hom.: 2 Cov.: 34 AF XY: 0.000421 AC XY: 306AN XY: 727232
GnomAD4 genome AF: 0.00524 AC: 797AN: 152158Hom.: 14 Cov.: 31 AF XY: 0.00489 AC XY: 364AN XY: 74372
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Sep 29, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at