rs61747868
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_012293.3(PXDN):c.4088G>A(p.Gly1363Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00165 in 1,613,980 control chromosomes in the GnomAD database, including 29 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 Likely benign (★★).
Frequency
Consequence
NM_012293.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PXDN | NM_012293.3 | c.4088G>A | p.Gly1363Glu | missense_variant | 21/23 | ENST00000252804.9 | NP_036425.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PXDN | ENST00000252804.9 | c.4088G>A | p.Gly1363Glu | missense_variant | 21/23 | 1 | NM_012293.3 | ENSP00000252804.4 | ||
PXDN | ENST00000478155.5 | n.3176G>A | non_coding_transcript_exon_variant | 13/15 | 2 | |||||
PXDN | ENST00000453308.1 | n.224+338G>A | intron_variant | 3 | ENSP00000414098.1 |
Frequencies
GnomAD3 genomes AF: 0.00723 AC: 1100AN: 152194Hom.: 14 Cov.: 33
GnomAD3 exomes AF: 0.00215 AC: 536AN: 249244Hom.: 5 AF XY: 0.00173 AC XY: 234AN XY: 135222
GnomAD4 exome AF: 0.00106 AC: 1550AN: 1461668Hom.: 15 Cov.: 35 AF XY: 0.000983 AC XY: 715AN XY: 727124
GnomAD4 genome AF: 0.00726 AC: 1106AN: 152312Hom.: 14 Cov.: 33 AF XY: 0.00714 AC XY: 532AN XY: 74482
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 14, 2023 | See Variant Classification Assertion Criteria. - |
Likely benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
Anterior segment dysgenesis 7 Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jul 26, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at