chr14-73251718-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001365906.3(PAPLN):c.725C>T(p.Ala242Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000107 in 1,613,280 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001365906.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PAPLN | NM_001365906.3 | c.725C>T | p.Ala242Val | missense_variant | 9/27 | ENST00000644200.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PAPLN | ENST00000644200.2 | c.725C>T | p.Ala242Val | missense_variant | 9/27 | NM_001365906.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152180Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000801 AC: 20AN: 249674Hom.: 1 AF XY: 0.0000739 AC XY: 10AN XY: 135392
GnomAD4 exome AF: 0.000110 AC: 161AN: 1460982Hom.: 0 Cov.: 33 AF XY: 0.0000949 AC XY: 69AN XY: 726780
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152298Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74472
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 25, 2023 | The c.644C>T (p.A215V) alteration is located in exon 8 (coding exon 7) of the PAPLN gene. This alteration results from a C to T substitution at nucleotide position 644, causing the alanine (A) at amino acid position 215 to be replaced by a valine (V). 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