19-54118311-C-G
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_015629.4(PRPF31):āc.33C>Gā(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 (ā ).
Frequency
Genomes: š 0.000020 ( 0 hom., cov: 32)
Exomes š: 0.0000055 ( 0 hom. )
Consequence
PRPF31
NM_015629.4 synonymous
NM_015629.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.68
Genes affected
PRPF31 (HGNC:15446): (pre-mRNA processing factor 31) This gene encodes a component of the spliceosome complex and is one of several retinitis pigmentosa-causing genes. When the gene product is added to the spliceosome complex, activation occurs.[provided by RefSeq, Jan 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.56).
BP6
Variant 19-54118311-C-G is Benign according to our data. Variant chr19-54118311-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 2038438.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.68 with no splicing effect.
BS2
High AC in GnomAdExome4 at 8 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRPF31 | NM_015629.4 | c.33C>G | p.Leu11= | synonymous_variant | 2/14 | ENST00000321030.9 | NP_056444.3 | |
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 | XP_006723200.1 | ||
PRPF31 | XM_047438587.1 | c.33C>G | p.Leu11= | synonymous_variant | 2/10 | XP_047294543.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRPF31 | ENST00000321030.9 | c.33C>G | p.Leu11= | synonymous_variant | 2/14 | 1 | NM_015629.4 | ENSP00000324122 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000198 AC: 3AN: 151824Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249020Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134804
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GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461388Hom.: 0 Cov.: 33 AF XY: 0.00000825 AC XY: 6AN XY: 726982
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GnomAD4 genome AF: 0.0000198 AC: 3AN: 151824Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74124
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jun 01, 2022 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at