5-140821897-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_018908.3(PCDHA5):āc.122G>Cā(p.Gly41Ala) variant causes a missense change. The variant allele was found at a frequency of 0.00000805 in 1,614,240 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_018908.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PCDHA5 | NM_018908.3 | c.122G>C | p.Gly41Ala | missense_variant | Exon 1 of 4 | ENST00000529859.2 | NP_061731.1 | |
PCDHA1 | NM_018900.4 | c.2394+33213G>C | intron_variant | Intron 1 of 3 | ENST00000504120.4 | NP_061723.1 | ||
PCDHA3 | NM_018906.3 | c.2394+18306G>C | intron_variant | Intron 1 of 3 | ENST00000522353.3 | NP_061729.1 | ||
PCDHA2 | NM_018905.3 | c.2388+24545G>C | intron_variant | Intron 1 of 3 | ENST00000526136.2 | NP_061728.1 | ||
PCDHA4 | NM_018907.4 | c.2385+12325G>C | intron_variant | Intron 1 of 3 | ENST00000530339.2 | NP_061730.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PCDHA5 | ENST00000529859.2 | c.122G>C | p.Gly41Ala | missense_variant | Exon 1 of 4 | 1 | NM_018908.3 | ENSP00000436557.1 | ||
PCDHA1 | ENST00000504120.4 | c.2394+33213G>C | intron_variant | Intron 1 of 3 | 1 | NM_018900.4 | ENSP00000420840.3 | |||
PCDHA3 | ENST00000522353.3 | c.2394+18306G>C | intron_variant | Intron 1 of 3 | 1 | NM_018906.3 | ENSP00000429808.2 | |||
PCDHA2 | ENST00000526136.2 | c.2388+24545G>C | intron_variant | Intron 1 of 3 | 1 | NM_018905.3 | ENSP00000431748.1 | |||
PCDHA4 | ENST00000530339.2 | c.2385+12325G>C | intron_variant | Intron 1 of 3 | 1 | NM_018907.4 | ENSP00000435300.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152252Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251428Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135916
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461870Hom.: 0 Cov.: 35 AF XY: 0.00000963 AC XY: 7AN XY: 727236
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152370Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74518
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.122G>C (p.G41A) alteration is located in exon 1 (coding exon 1) of the PCDHA5 gene. This alteration results from a G to C substitution at nucleotide position 122, causing the glycine (G) at amino acid position 41 to be replaced by an alanine (A). 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