2-1648187-C-T
Variant summary
Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_012293.3(PXDN):c.3593G>A(p.Arg1198Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0024 in 1,611,760 control chromosomes in the GnomAD database, including 82 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1198W) has been classified as Uncertain significance.
Frequency
Consequence
NM_012293.3 missense
Scores
Clinical Significance
Conservation
Publications
- anterior segment dysgenesis 7Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: G2P, PanelApp Australia, ClinGen, Orphanet, Ambry Genetics, Labcorp Genetics (formerly Invitae)
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ACMG classification
Our verdict: Benign. The variant received -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PXDN | NM_012293.3 | c.3593G>A | p.Arg1198Gln | missense_variant | Exon 17 of 23 | ENST00000252804.9 | NP_036425.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0124 AC: 1886AN: 152118Hom.: 39 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.00331 AC: 816AN: 246852 AF XY: 0.00251 show subpopulations
GnomAD4 exome AF: 0.00136 AC: 1980AN: 1459524Hom.: 43 Cov.: 31 AF XY: 0.00114 AC XY: 824AN XY: 725584 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.0124 AC: 1891AN: 152236Hom.: 39 Cov.: 33 AF XY: 0.0119 AC XY: 886AN XY: 74434 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not provided Benign:2
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Anterior segment dysgenesis 7 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at