chr19-54118311-C-G
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_015629.4(PRPF31):c.33C>G(p.Leu11=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000682 in 1,613,212 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. L11L) has been classified as Uncertain significance.
Frequency
Consequence
NM_015629.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRPF31 | NM_015629.4 | c.33C>G | p.Leu11= | synonymous_variant | 2/14 | ENST00000321030.9 | |
PRPF31-AS1 | XR_007067340.1 | n.1843-632G>C | intron_variant, non_coding_transcript_variant | ||||
PRPF31 | XM_006723137.5 | c.33C>G | p.Leu11= | synonymous_variant | 2/14 | ||
PRPF31 | XM_047438587.1 | c.33C>G | p.Leu11= | synonymous_variant | 2/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRPF31 | ENST00000321030.9 | c.33C>G | p.Leu11= | synonymous_variant | 2/14 | 1 | NM_015629.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000198 AC: 3AN: 151824Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249020Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134804
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461388Hom.: 0 Cov.: 33 AF XY: 0.00000825 AC XY: 6AN XY: 726982
GnomAD4 genome ? AF: 0.0000198 AC: 3AN: 151824Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74124
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 01, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at