10-70533928-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_014431.3(PALD1):c.877C>T(p.Pro293Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000764 in 1,596,136 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014431.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PALD1 | NM_014431.3 | c.877C>T | p.Pro293Ser | missense_variant | 8/20 | ENST00000263563.7 | NP_055246.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PALD1 | ENST00000263563.7 | c.877C>T | p.Pro293Ser | missense_variant | 8/20 | 1 | NM_014431.3 | ENSP00000263563 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152244Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000549 AC: 13AN: 236998Hom.: 0 AF XY: 0.0000624 AC XY: 8AN XY: 128184
GnomAD4 exome AF: 0.0000776 AC: 112AN: 1443892Hom.: 0 Cov.: 31 AF XY: 0.0000963 AC XY: 69AN XY: 716624
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152244Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74380
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 22, 2024 | The c.877C>T (p.P293S) alteration is located in exon 8 (coding exon 7) of the PALD1 gene. This alteration results from a C to T substitution at nucleotide position 877, causing the proline (P) at amino acid position 293 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