chr9-116154389-C-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_002581.5(PAPPA):c.217C>A(p.Arg73Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00001 in 1,100,418 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002581.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000202 AC: 3AN: 148466Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000840 AC: 8AN: 951952Hom.: 0 Cov.: 13 AF XY: 0.00000437 AC XY: 2AN XY: 457504
GnomAD4 genome AF: 0.0000202 AC: 3AN: 148466Hom.: 0 Cov.: 32 AF XY: 0.0000276 AC XY: 2AN XY: 72366
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.217C>A (p.R73S) alteration is located in exon 1 (coding exon 1) of the PAPPA gene. This alteration results from a C to A substitution at nucleotide position 217, causing the arginine (R) at amino acid position 73 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