chr8-51319927-G-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_144651.5(PXDNL):c.4356C>A(p.Asp1452Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 1,555,250 control chromosomes in the GnomAD database, including 60,980 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_144651.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PXDNL | NM_144651.5 | c.4356C>A | p.Asp1452Glu | missense_variant | 23/23 | ENST00000356297.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PXDNL | ENST00000356297.5 | c.4356C>A | p.Asp1452Glu | missense_variant | 23/23 | 1 | NM_144651.5 | P1 | |
ENST00000521294.1 | n.121-793G>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.339 AC: 51471AN: 151862Hom.: 10489 Cov.: 32
GnomAD3 exomes AF: 0.254 AC: 54271AN: 213490Hom.: 8012 AF XY: 0.250 AC XY: 29320AN XY: 117058
GnomAD4 exome AF: 0.261 AC: 366154AN: 1403270Hom.: 50462 Cov.: 32 AF XY: 0.259 AC XY: 180855AN XY: 697108
GnomAD4 genome ? AF: 0.339 AC: 51555AN: 151980Hom.: 10518 Cov.: 32 AF XY: 0.332 AC XY: 24636AN XY: 74316
ClinVar
Submissions by phenotype
PXDNL-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 28, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at