5-140795881-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_018905.3(PCDHA2):c.917G>A(p.Gly306Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000744 in 1,613,818 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018905.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCDHA2 | NM_018905.3 | c.917G>A | p.Gly306Glu | missense_variant | 1/4 | ENST00000526136.2 | |
PCDHA1 | NM_018900.4 | c.2394+7197G>A | intron_variant | ENST00000504120.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCDHA2 | ENST00000526136.2 | c.917G>A | p.Gly306Glu | missense_variant | 1/4 | 1 | NM_018905.3 | P1 | |
PCDHA1 | ENST00000504120.4 | c.2394+7197G>A | intron_variant | 1 | NM_018900.4 | P1 | |||
ENST00000655235.1 | n.658-7027C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152110Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251110Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135804
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461708Hom.: 0 Cov.: 33 AF XY: 0.00000825 AC XY: 6AN XY: 727148
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152110Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74290
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 27, 2022 | The c.917G>A (p.G306E) alteration is located in exon 1 (coding exon 1) of the PCDHA2 gene. This alteration results from a G to A substitution at nucleotide position 917, causing the glycine (G) at amino acid position 306 to be replaced by a glutamic acid (E). 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