5-140808762-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_018907.4(PCDHA4):c.1575C>A(p.His525Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000136 in 1,612,106 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_018907.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCDHA4 | NM_018907.4 | c.1575C>A | p.His525Gln | missense_variant | 1/4 | ENST00000530339.2 | |
PCDHA1 | NM_018900.4 | c.2394+20078C>A | intron_variant | ENST00000504120.4 | |||
PCDHA2 | NM_018905.3 | c.2388+11410C>A | intron_variant | ENST00000526136.2 | |||
PCDHA3 | NM_018906.3 | c.2394+5171C>A | intron_variant | ENST00000522353.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCDHA4 | ENST00000530339.2 | c.1575C>A | p.His525Gln | missense_variant | 1/4 | 1 | NM_018907.4 | P1 | |
PCDHA1 | ENST00000504120.4 | c.2394+20078C>A | intron_variant | 1 | NM_018900.4 | P1 | |||
PCDHA3 | ENST00000522353.3 | c.2394+5171C>A | intron_variant | 1 | NM_018906.3 | P1 | |||
PCDHA2 | ENST00000526136.2 | c.2388+11410C>A | intron_variant | 1 | NM_018905.3 | P1 | |||
ENST00000655235.1 | n.657+19131G>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152198Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 250754Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135618
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1459908Hom.: 0 Cov.: 36 AF XY: 0.0000138 AC XY: 10AN XY: 726292
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152198Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 05, 2023 | The c.1575C>A (p.H525Q) alteration is located in exon 1 (coding exon 1) of the PCDHA4 gene. This alteration results from a C to A substitution at nucleotide position 1575, causing the histidine (H) at amino acid position 525 to be replaced by a glutamine (Q). 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