12-63624101-G-A
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PM5PP3_ModeratePP5
The ENST00000324472.9(DPY19L2):c.892C>T(p.Arg298Cys) variant causes a missense change. The variant allele was found at a frequency of 0.00000745 in 1,611,592 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R298H) has been classified as Pathogenic.
Frequency
Consequence
ENST00000324472.9 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DPY19L2 | NM_173812.5 | c.892C>T | p.Arg298Cys | missense_variant | 8/22 | ENST00000324472.9 | NP_776173.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DPY19L2 | ENST00000324472.9 | c.892C>T | p.Arg298Cys | missense_variant | 8/22 | 1 | NM_173812.5 | ENSP00000315988 | P1 | |
DPY19L2 | ENST00000306389.7 | c.*344+2368C>T | intron_variant, NMD_transcript_variant | 1 | ENSP00000445878 | |||||
ENST00000509615.2 | n.239-277C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151994Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250872Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135604
GnomAD4 exome AF: 0.00000685 AC: 10AN: 1459480Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 726054
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152112Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74340
ClinVar
Submissions by phenotype
Spermatogenic failure 9 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Aug 15, 2012 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at