chr5-140795178-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018905.3(PCDHA2):c.214G>A(p.Gly72Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,613,966 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCDHA2 | NM_018905.3 | c.214G>A | p.Gly72Arg | missense_variant | 1/4 | ENST00000526136.2 | |
PCDHA1 | NM_018900.4 | c.2394+6494G>A | intron_variant | ENST00000504120.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCDHA2 | ENST00000526136.2 | c.214G>A | p.Gly72Arg | missense_variant | 1/4 | 1 | NM_018905.3 | P1 | |
PCDHA1 | ENST00000504120.4 | c.2394+6494G>A | intron_variant | 1 | NM_018900.4 | P1 | |||
ENST00000655235.1 | n.658-6324C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152232Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000801 AC: 2AN: 249570Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135370
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461734Hom.: 0 Cov.: 185 AF XY: 0.00000688 AC XY: 5AN XY: 727164
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152232Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74376
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 15, 2021 | The c.214G>A (p.G72R) 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 214, causing the glycine (G) at amino acid position 72 to be replaced by an arginine (R). 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