chr10-70533946-C-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_014431.3(PALD1):c.895C>T(p.Arg299Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00306 in 1,607,480 control chromosomes in the GnomAD database, including 12 homozygotes. 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 Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R299H) has been classified as Uncertain significance.
Frequency
Consequence
NM_014431.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PALD1 | NM_014431.3 | c.895C>T | p.Arg299Cys | missense_variant | 8/20 | ENST00000263563.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PALD1 | ENST00000263563.7 | c.895C>T | p.Arg299Cys | missense_variant | 8/20 | 1 | NM_014431.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00212 AC: 323AN: 152238Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00239 AC: 584AN: 244842Hom.: 5 AF XY: 0.00239 AC XY: 317AN XY: 132604
GnomAD4 exome AF: 0.00316 AC: 4601AN: 1455124Hom.: 11 Cov.: 31 AF XY: 0.00306 AC XY: 2211AN XY: 723472
GnomAD4 genome AF: 0.00212 AC: 323AN: 152356Hom.: 1 Cov.: 33 AF XY: 0.00172 AC XY: 128AN XY: 74498
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Mar 29, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at