1-52415362-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_032864.4(PRPF38A):c.872G>A(p.Arg291Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000159 in 1,613,800 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 Uncertain significance (★).
Frequency
Consequence
NM_032864.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRPF38A | ENST00000257181.10 | c.872G>A | p.Arg291Lys | missense_variant | Exon 9 of 10 | 1 | NM_032864.4 | ENSP00000257181.8 | ||
PRPF38A | ENST00000474048.1 | n.660G>A | non_coding_transcript_exon_variant | Exon 7 of 8 | 1 | |||||
TUT4 | ENST00000528457.5 | c.374-6902C>T | intron_variant | Intron 2 of 2 | 3 | ENSP00000432475.1 | ||||
TUT4 | ENST00000527941.5 | n.*68-5756C>T | intron_variant | Intron 3 of 4 | 5 | ENSP00000436810.1 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152148Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000796 AC: 20AN: 251342Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135846
GnomAD4 exome AF: 0.000168 AC: 246AN: 1461652Hom.: 0 Cov.: 30 AF XY: 0.000142 AC XY: 103AN XY: 727142
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152148Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.872G>A (p.R291K) alteration is located in exon 9 (coding exon 9) of the PRPF38A gene. This alteration results from a G to A substitution at nucleotide position 872, causing the arginine (R) at amino acid position 291 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at