chr2-152717424-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001365597.4(PRPF40A):c.16G>A(p.Gly6Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000409 in 1,613,830 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 10/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001365597.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRPF40A | NM_001365597.4 | c.16G>A | p.Gly6Ser | missense_variant | 1/26 | ENST00000545856.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRPF40A | ENST00000545856.8 | c.16G>A | p.Gly6Ser | missense_variant | 1/26 | 1 | NM_001365597.4 | P3 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152216Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000137 AC: 34AN: 248206Hom.: 0 AF XY: 0.000133 AC XY: 18AN XY: 134958
GnomAD4 exome AF: 0.0000404 AC: 59AN: 1461496Hom.: 0 Cov.: 30 AF XY: 0.0000468 AC XY: 34AN XY: 727044
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152334Hom.: 0 Cov.: 33 AF XY: 0.0000806 AC XY: 6AN XY: 74484
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 22, 2023 | The c.16G>A (p.G6S) alteration is located in exon 1 (coding exon 1) of the PRPF40A gene. This alteration results from a G to A substitution at nucleotide position 16, causing the glycine (G) at amino acid position 6 to be replaced by a serine (S). 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