8-51345869-A-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_144651.5(PXDNL):c.3980T>A(p.Val1327Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0193 in 1,612,452 control chromosomes in the GnomAD database, including 724 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 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.3980T>A | p.Val1327Asp | missense_variant | 20/23 | ENST00000356297.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PXDNL | ENST00000356297.5 | c.3980T>A | p.Val1327Asp | missense_variant | 20/23 | 1 | NM_144651.5 | P1 | |
PXDNL | ENST00000522933.5 | c.1202T>A | p.Val401Asp | missense_variant | 3/6 | 5 | |||
PXDNL | ENST00000522628.5 | c.1700-24972T>A | intron_variant, NMD_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0408 AC: 6216AN: 152194Hom.: 265 Cov.: 32
GnomAD3 exomes AF: 0.0209 AC: 5210AN: 248980Hom.: 154 AF XY: 0.0202 AC XY: 2724AN XY: 135052
GnomAD4 exome AF: 0.0170 AC: 24876AN: 1460140Hom.: 458 Cov.: 29 AF XY: 0.0173 AC XY: 12536AN XY: 726482
GnomAD4 genome ? AF: 0.0409 AC: 6224AN: 152312Hom.: 266 Cov.: 32 AF XY: 0.0396 AC XY: 2948AN XY: 74494
ClinVar
Submissions by phenotype
PXDNL-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 14, 2020 | 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