20-63981306-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The NM_012469.4(PRPF6):c.61C>T(p.Leu21Leu) variant causes a synonymous change. The variant allele was found at a frequency of 0.0000817 in 1,602,606 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_012469.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRPF6 | NM_012469.4 | c.61C>T | p.Leu21Leu | synonymous_variant | Exon 1 of 21 | ENST00000266079.5 | NP_036601.2 | |
PRPF6 | XM_006723769.4 | c.61C>T | p.Leu21Leu | synonymous_variant | Exon 1 of 20 | XP_006723832.1 | ||
PRPF6 | XR_007067448.1 | n.175C>T | non_coding_transcript_exon_variant | Exon 1 of 20 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152176Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000139 AC: 31AN: 222780Hom.: 0 AF XY: 0.000131 AC XY: 16AN XY: 121732
GnomAD4 exome AF: 0.0000793 AC: 115AN: 1450430Hom.: 1 Cov.: 31 AF XY: 0.0000860 AC XY: 62AN XY: 720604
GnomAD4 genome AF: 0.000105 AC: 16AN: 152176Hom.: 0 Cov.: 33 AF XY: 0.0000942 AC XY: 7AN XY: 74344
ClinVar
Submissions by phenotype
Retinitis pigmentosa Uncertain:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at