5-141339995-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_018915.4(PCDHGA2):c.1024G>A(p.Asp342Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000744 in 1,613,856 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018915.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PCDHGA2 | NM_018915.4 | c.1024G>A | p.Asp342Asn | missense_variant | Exon 1 of 4 | ENST00000394576.3 | NP_061738.1 | |
PCDHGA1 | NM_018912.3 | c.2421+6890G>A | intron_variant | Intron 1 of 3 | ENST00000517417.3 | NP_061735.1 | ||
PCDHGA2 | NM_032009.3 | c.1024G>A | p.Asp342Asn | missense_variant | Exon 1 of 1 | NP_114398.1 | ||
PCDHG@ | n.141339995G>A | intragenic_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PCDHGA2 | ENST00000394576.3 | c.1024G>A | p.Asp342Asn | missense_variant | Exon 1 of 4 | 1 | NM_018915.4 | ENSP00000378077.2 | ||
PCDHGA1 | ENST00000517417.3 | c.2421+6890G>A | intron_variant | Intron 1 of 3 | 1 | NM_018912.3 | ENSP00000431083.1 | |||
PCDHGA2 | ENST00000528330.2 | c.1024G>A | p.Asp342Asn | missense_variant | Exon 1 of 1 | 6 | ENSP00000483020.1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152070Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461786Hom.: 0 Cov.: 34 AF XY: 0.00000413 AC XY: 3AN XY: 727198
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152070Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74296
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1024G>A (p.D342N) alteration is located in exon 1 (coding exon 1) of the PCDHGA2 gene. This alteration results from a G to A substitution at nucleotide position 1024, causing the aspartic acid (D) at amino acid position 342 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at